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source: trunk/GSASIIphsGUI.py @ 1486

Last change on this file since 1486 was 1486, checked in by toby, 9 years ago
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1	# -- coding: utf-8 --
2	#GSASII - phase data display routines
3	########### SVN repository information ###################
4	# $Date: 2014-09-04 17:35:40 +0000 (Thu, 04 Sep 2014) $
5	# $Author: toby $
6	# $Revision: 1486 $
7	# $URL: trunk/GSASIIphsGUI.py $
8	# $Id: GSASIIphsGUI.py 1486 2014-09-04 17:35:40Z toby $
9	########### SVN repository information ###################
10	'''
11	GSASIIphsGUI: Phase GUI
12	-------------------------
13
14	Module to create the GUI for display of phase information
15	in the data display window when a phase is selected.
16	Phase information is stored in one or more
17	:ref:`Phase Tree Item <Phase_table>` objects.
18	Note that there are functions
19	that respond to some tabs in the phase GUI in other modules
20	(such as GSASIIddata).
21
22	'''
23	import os.path
24	import wx
25	import wx.grid as wg
26	import wx.lib.gridmovers as wgmove
27	import wx.wizard as wz
28	import wx.lib.scrolledpanel as wxscroll
29	import matplotlib as mpl
30	import math
31	import copy
32	import time
33	import sys
34	import random as ran
35	import cPickle
36	import GSASIIpath
37	GSASIIpath.SetVersionNumber("$Revision: 1486 $")
38	import GSASIIlattice as G2lat
39	import GSASIIspc as G2spc
40	import GSASIIElem as G2elem
41	import GSASIIElemGUI as G2elemGUI
42	import GSASIIddataGUI as G2ddG
43	import GSASIIplot as G2plt
44	import GSASIIgrid as G2gd
45	import GSASIIIO as G2IO
46	import GSASIIstrMain as G2stMn
47	import GSASIImath as G2mth
48	import GSASIIpwd as G2pwd
49	import GSASIIpy3 as G2py3
50	import GSASIIobj as G2obj
51	import numpy as np
52	import numpy.linalg as nl
53	import numpy.ma as ma
54
55	VERY_LIGHT_GREY = wx.Colour(235,235,235)
56	WHITE = wx.Colour(255,255,255)
57	BLACK = wx.Colour(0,0,0)
58	WACV = wx.ALIGN_CENTER_VERTICAL
59	mapDefault = {'MapType':'','RefList':'','Resolution':0.5,'Show bonds':True,
60	'rho':[],'rhoMax':0.,'mapSize':10.0,'cutOff':50.,'Flip':False}
61	# trig functions in degrees
62	sind = lambda x: np.sin(x*np.pi/180.)
63	tand = lambda x: np.tan(x*np.pi/180.)
64	cosd = lambda x: np.cos(x*np.pi/180.)
65	asind = lambda x: 180.*np.arcsin(x)/np.pi
66	acosd = lambda x: 180.*np.arccos(x)/np.pi
67
68	def SetPhaseWindow(mainFrame,phasePage,mainSizer):
69	phasePage.SetSizer(mainSizer)
70	Size = mainSizer.GetMinSize()
71	Size[0] += 40
72	# Size[1] = 500
73	Size[1] = min(Size[1]+ 150,500)
74	phasePage.SetSize(Size)
75	phasePage.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1)
76	mainFrame.setSizePosLeft(Size)
77
78	def UpdatePhaseData(G2frame,Item,data,oldPage):
79	'''Create the data display window contents when a phase is clicked on
80	in the main (data tree) window.
81	Called only from :meth:`GSASIIgrid.MovePatternTreeToGrid`,
82	which in turn is called from :meth:`GSASII.GSASII.OnPatternTreeSelChanged`
83	when a tree item is selected.
84
85	:param wx.frame G2frame: the main GSAS-II frame object
86	:param wx.TreeItemId Item: the tree item that was selected
87	:param dict data: all the information on the phase in a dictionary
88	:param int oldPage: This sets a tab to select when moving
89	from one phase to another, in which case the same tab is selected
90	to display first. This is set only when the previous data tree
91	selection is a phase, if not the value is None. The default action
92	is to bring up the General tab.
93
94	'''
95
96	# UpdatePhaseData execution continues below
97
98	def SetupGeneral():
99	generalData = data['General']
100	atomData = data['Atoms']
101	generalData['AtomTypes'] = []
102	generalData['Isotopes'] = {}
103	# various patches
104	if 'Isotope' not in generalData:
105	generalData['Isotope'] = {}
106	if 'Data plot type' not in generalData:
107	generalData['Data plot type'] = 'Mustrain'
108	if 'POhkl' not in generalData:
109	generalData['POhkl'] = [0,0,1]
110	if 'Map' not in generalData:
111	generalData['Map'] = mapDefault
112	if 'Flip' not in generalData:
113	generalData['Flip'] = {'RefList':'','Resolution':0.5,'Norm element':'None',
114	'k-factor':0.1,'k-Max':20.}
115	if 'doPawley' not in generalData:
116	generalData['doPawley'] = False
117	if 'Pawley dmin' not in generalData:
118	generalData['Pawley dmin'] = 1.0
119	if 'Pawley neg wt' not in generalData:
120	generalData['Pawley neg wt'] = 0.0
121	if 'Algolrithm' in generalData.get('MCSA controls',{}) or \
122	'MCSA controls' not in generalData:
123	generalData['MCSA controls'] = {'Data source':'','Annealing':[50.,0.001,50],
124	'dmin':2.0,'Algorithm':'log','Jump coeff':[0.95,0.5],'boltzmann':1.0,
125	'fast parms':[1.0,1.0,1.0],'log slope':0.9,'Cycles':1,'Results':[],'newDmin':True}
126	if 'AtomPtrs' not in generalData:
127	generalData['AtomPtrs'] = [3,1,7,9]
128	if generalData['Type'] =='macromolecular':
129	generalData['AtomPtrs'] = [6,4,10,12]
130	# end of patches
131	cx,ct,cs,cia = generalData['AtomPtrs']
132	generalData['NoAtoms'] = {}
133	generalData['BondRadii'] = []
134	generalData['AngleRadii'] = []
135	generalData['vdWRadii'] = []
136	generalData['AtomMass'] = []
137	generalData['Color'] = []
138	generalData['Mydir'] = G2frame.dirname
139	for atom in atomData:
140	atom[ct] = atom[ct].lower().capitalize() #force to standard form
141	if generalData['AtomTypes'].count(atom[ct]):
142	generalData['NoAtoms'][atom[ct]] += atom[cs-1]*float(atom[cs+1])
143	elif atom[ct] != 'UNK':
144	Info = G2elem.GetAtomInfo(atom[ct])
145	generalData['AtomTypes'].append(atom[ct])
146	generalData['Z'] = Info['Z']
147	generalData['Isotopes'][atom[ct]] = Info['Isotopes']
148	generalData['BondRadii'].append(Info['Drad'])
149	generalData['AngleRadii'].append(Info['Arad'])
150	generalData['vdWRadii'].append(Info['Vdrad'])
151	if atom[ct] in generalData['Isotope']:
152	generalData['AtomMass'].append(Info['Isotopes'][generalData['Isotope'][atom[ct]]]['Mass'])
153	else:
154	generalData['Isotope'][atom[ct]] = 'Nat. Abund.'
155	generalData['AtomMass'].append(Info['Mass'])
156	generalData['NoAtoms'][atom[ct]] = atom[cs-1]*float(atom[cs+1])
157	generalData['Color'].append(Info['Color'])
158	F000X = 0.
159	F000N = 0.
160	for i,elem in enumerate(generalData['AtomTypes']):
161	F000X += generalData['NoAtoms'][elem]*generalData['Z']
162	isotope = generalData['Isotope'][elem]
163	F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
164	generalData['F000X'] = F000X
165	generalData['F000N'] = F000N
166
167
168	################################################################################
169	##### General phase routines
170	################################################################################
171
172	def UpdateGeneral():
173	'''Draw the controls for the General phase data subpage
174	'''
175
176	""" This is the default dictionary structure for phase data
177	(taken from GSASII.py)
178	'General':{
179	'Name':PhaseName
180	'Type':'nuclear'
181	'SGData':SGData
182	'Cell':[False,10.,10.,10.,90.,90.,90,1000.]
183	'AtomPtrs':[]
184	'Histogram list':['',]
185	'Pawley dmin':1.0,
186	'Pawley neg wt':0.0}
187	'Atoms':[]
188	'Drawing':{}
189	"""
190	# UpdateGeneral execution starts here
191	phaseTypes = ['nuclear','modulated','magnetic','macromolecular']
192	SetupGeneral()
193	generalData = data['General']
194	Map = generalData['Map']
195	Flip = generalData['Flip']
196	MCSAdata = generalData['MCSA controls']
197	PWDR = any(['PWDR' in item for item in data['Histograms'].keys()])
198	# UpdateGeneral execution continues below
199
200	def NameSizer():
201	def OnPhaseName(event):
202	oldName = generalData['Name']
203	generalData['Name'] = NameTxt.GetValue()
204	G2frame.G2plotNB.Rename(oldName,generalData['Name'])
205	G2frame.dataFrame.SetLabel('Phase Data for '+generalData['Name'])
206	G2frame.PatternTree.SetItemText(Item,generalData['Name'])
207	#Hmm, need to change phase name key in Reflection Lists for each histogram
208
209	def OnPhaseType(event):
210	if not generalData['AtomTypes']: #can change only if no atoms!
211	generalData['Type'] = TypeTxt.GetValue()
212	wx.CallAfter(UpdateGeneral)
213	else:
214	TypeTxt.SetValue(generalData['Type'])
215
216	def OnSpaceGroup(event):
217	SpcGp = SGTxt.GetValue()
218	SGErr,SGData = G2spc.SpcGroup(SpcGp)
219	# try a lookup on the user-supplied name
220	if SGErr:
221	SpGrpNorm = G2spc.StandardizeSpcName(SpcGp)
222	if SpGrpNorm:
223	E,SGData = G2spc.SpcGroup(SpGrpNorm)
224	if not E: SGErr = False
225	if SGErr:
226	text = [G2spc.SGErrors(SGErr)+'\nSpace Group set to previous']
227	SGTxt.SetValue(generalData['SGData']['SpGrp'])
228	msg = 'Space Group Error'
229	Style = wx.ICON_EXCLAMATION
230	else:
231	text = G2spc.SGPrint(SGData)
232	generalData['SGData'] = SGData
233	msg = 'Space Group Information'
234	Style = wx.ICON_INFORMATION
235	Text = ''
236	for line in text:
237	Text += line+'\n'
238	wx.MessageBox(Text,caption=msg,style=Style)
239	wx.CallAfter(UpdateGeneral)
240
241	nameSizer = wx.BoxSizer(wx.HORIZONTAL)
242	nameSizer.Add(wx.StaticText(General,-1,' Phase name: '),0,WACV)
243	NameTxt = wx.TextCtrl(General,-1,value=generalData['Name'],style=wx.TE_PROCESS_ENTER)
244	NameTxt.Bind(wx.EVT_TEXT_ENTER,OnPhaseName)
245	NameTxt.Bind(wx.EVT_KILL_FOCUS,OnPhaseName)
246	nameSizer.Add(NameTxt,0,WACV)
247	nameSizer.Add(wx.StaticText(General,-1,' Phase type: '),0,WACV)
248	TypeTxt = wx.ComboBox(General,-1,value=generalData['Type'],choices=phaseTypes,
249	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
250	TypeTxt.Bind(wx.EVT_COMBOBOX, OnPhaseType)
251	nameSizer.Add(TypeTxt,0,WACV)
252	nameSizer.Add(wx.StaticText(General,-1,' Space group: '),0,WACV)
253	SGTxt = wx.TextCtrl(General,-1,value=generalData['SGData']['SpGrp'],style=wx.TE_PROCESS_ENTER)
254	SGTxt.Bind(wx.EVT_TEXT_ENTER,OnSpaceGroup)
255	nameSizer.Add(SGTxt,0,WACV)
256	return nameSizer
257
258	def CellSizer():
259
260	cellGUIlist = [[['m3','m3m'],4,zip([" Unit cell: a = "," Vol = "],["%.5f","%.3f"],[True,False],[0,0])],
261	[['3R','3mR'],6,zip([" a = "," alpha = "," Vol = "],["%.5f","%.3f","%.3f"],[True,True,False],[0,2,0])],
262	[['3','3m1','31m','6/m','6/mmm','4/m','4/mmm'],6,zip([" a = "," c = "," Vol = "],["%.5f","%.5f","%.3f"],[True,True,False],[0,2,0])],
263	[['mmm'],8,zip([" a = "," b = "," c = "," Vol = "],["%.5f","%.5f","%.5f","%.3f"],
264	[True,True,True,False],[0,1,2,0])],
265	[['2/m'+'a'],10,zip([" a = "," b = "," c = "," alpha = "," Vol = "],
266	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,5,0])],
267	[['2/m'+'b'],10,zip([" a = "," b = "," c = "," beta = "," Vol = "],
268	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
269	[['2/m'+'c'],10,zip([" a = "," b = "," c = "," gamma = "," Vol = "],
270	["%.5f","%.5f","%.5f","%.3f","%.3f"],[True,True,True,True,False],[0,1,2,3,0])],
271	[['-1'],8,zip([" a = "," b = "," c = "," Vol = "," alpha = "," beta = "," gamma = "],
272	["%.5f","%.5f","%.5f","%.3f","%.3f","%.3f","%.3f"],
273	[True,True,True,False,True,True,True],[0,1,2,0,3,4,5])]]
274
275	def OnCellRef(event):
276	generalData['Cell'][0] = cellRef.GetValue()
277
278	def OnCellChange(event):
279	SGData = generalData['SGData']
280	laue = SGData['SGLaue']
281	if laue == '2/m':
282	laue += SGData['SGUniq']
283	cell = generalData['Cell']
284	Obj = event.GetEventObject()
285	ObjId = cellList.index(Obj.GetId())
286	try:
287	value = max(1.0,float(Obj.GetValue()))
288	except ValueError:
289	if ObjId < 3: #bad cell edge - reset
290	value = controls[6+ObjId]
291	else: #bad angle
292	value = 90.
293	if laue in ['m3','m3m']:
294	cell[1] = cell[2] = cell[3] = value
295	cell[4] = cell[5] = cell[6] = 90.0
296	Obj.SetValue("%.5f"%(cell[1]))
297	elif laue in ['3R','3mR']:
298	if ObjId == 0:
299	cell[1] = cell[2] = cell[3] = value
300	Obj.SetValue("%.5f"%(cell[1]))
301	else:
302	cell[4] = cell[5] = cell[6] = value
303	Obj.SetValue("%.5f"%(cell[4]))
304	elif laue in ['3','3m1','31m','6/m','6/mmm','4/m','4/mmm']:
305	cell[4] = cell[5] = 90.
306	cell[6] = 120.
307	if laue in ['4/m','4/mmm']:
308	cell[6] = 90.
309	if ObjId == 0:
310	cell[1] = cell[2] = value
311	Obj.SetValue("%.5f"%(cell[1]))
312	else:
313	cell[3] = value
314	Obj.SetValue("%.5f"%(cell[3]))
315	elif laue in ['mmm']:
316	cell[ObjId+1] = value
317	cell[4] = cell[5] = cell[6] = 90.
318	Obj.SetValue("%.5f"%(cell[ObjId+1]))
319	elif laue in ['2/m'+'a']:
320	cell[5] = cell[6] = 90.
321	if ObjId != 3:
322	cell[ObjId+1] = value
323	Obj.SetValue("%.5f"%(cell[ObjId+1]))
324	else:
325	cell[4] = value
326	Obj.SetValue("%.3f"%(cell[4]))
327	elif laue in ['2/m'+'b']:
328	cell[4] = cell[6] = 90.
329	if ObjId != 3:
330	cell[ObjId+1] = value
331	Obj.SetValue("%.5f"%(cell[ObjId+1]))
332	else:
333	cell[5] = value
334	Obj.SetValue("%.3f"%(cell[5]))
335	elif laue in ['2/m'+'c']:
336	cell[5] = cell[6] = 90.
337	if ObjId != 3:
338	cell[ObjId+1] = value
339	Obj.SetValue("%.5f"%(cell[ObjId+1]))
340	else:
341	cell[6] = value
342	Obj.SetValue("%.3f"%(cell[6]))
343	else:
344	cell[ObjId+1] = value
345	if ObjId < 3:
346	Obj.SetValue("%.5f"%(cell[1+ObjId]))
347	else:
348	Obj.SetValue("%.3f"%(cell[1+ObjId]))
349	cell[7] = G2lat.calc_V(G2lat.cell2A(cell[1:7]))
350	volVal.SetValue("%.3f"%(cell[7]))
351	density,mattCoeff = G2mth.getDensity(generalData)
352	if denSizer:
353	denSizer[1].SetValue('%.3f'%(density))
354	if denSizer[2]:
355	denSizer[2].SetValue('%.3f'%(mattCoeff))
356	generalData['Cell'] = cell
357
358	cell = generalData['Cell']
359	laue = generalData['SGData']['SGLaue']
360	if laue == '2/m':
361	laue += generalData['SGData']['SGUniq']
362	for cellGUI in cellGUIlist:
363	if laue in cellGUI[0]:
364	useGUI = cellGUI
365	cellSizer = wx.FlexGridSizer(0,useGUI[1]+1,5,5)
366	if PWDR:
367	cellRef = wx.CheckBox(General,-1,label='Refine unit cell:')
368	cellSizer.Add(cellRef,0,WACV)
369	cellRef.Bind(wx.EVT_CHECKBOX, OnCellRef)
370	cellRef.SetValue(cell[0])
371	cellList = []
372	for txt,fmt,ifEdit,Id in useGUI[2]:
373	cellSizer.Add(wx.StaticText(General,label=txt),0,WACV)
374	if ifEdit: #a,b,c,etc.
375	cellVal = wx.TextCtrl(General,value=(fmt%(cell[Id+1])),
376	style=wx.TE_PROCESS_ENTER)
377	cellVal.Bind(wx.EVT_TEXT_ENTER,OnCellChange)
378	cellVal.Bind(wx.EVT_KILL_FOCUS,OnCellChange)
379	cellSizer.Add(cellVal,0,WACV)
380	cellList.append(cellVal.GetId())
381	else: #volume
382	volVal = wx.TextCtrl(General,value=(fmt%(cell[7])),style=wx.TE_READONLY)
383	volVal.SetBackgroundColour(VERY_LIGHT_GREY)
384	cellSizer.Add(volVal,0,WACV)
385	return cellSizer
386
387	def ElemSizer():
388
389	def OnIsotope(event): #how can I update Atom weight on isotope change?
390	Obj = event.GetEventObject()
391	item = Indx[Obj.GetId()]
392	isotope = Obj.GetValue()
393	generalData['Isotope'][item] = isotope
394	indx = generalData['AtomTypes'].index(item)
395	data['General']['AtomMass'][indx] = generalData['Isotopes'][item][isotope]['Mass']
396	density,mattCoeff = G2mth.getDensity(generalData)
397	denSizer[1].SetValue('%.3f'%(density))
398	if denSizer[2]:
399	denSizer[2].SetValue('%.3f'%(mattCoeff))
400
401	elemSizer = wx.FlexGridSizer(0,len(generalData['AtomTypes'])+1,1,1)
402	elemSizer.Add(wx.StaticText(General,label=' Elements'),0,WACV)
403	for elem in generalData['AtomTypes']:
404	typTxt = wx.TextCtrl(General,value=elem,style=wx.TE_READONLY)
405	typTxt.SetBackgroundColour(VERY_LIGHT_GREY)
406	elemSizer.Add(typTxt,0,WACV)
407	elemSizer.Add(wx.StaticText(General,label=' Isotope'),0,WACV)
408	for elem in generalData['AtomTypes']:
409	choices = generalData['Isotopes'][elem].keys()
410	isoSel = wx.ComboBox(General,-1,value=generalData['Isotope'][elem],choices=choices,
411	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
412	isoSel.Bind(wx.EVT_COMBOBOX,OnIsotope)
413	Indx[isoSel.GetId()] = elem
414	elemSizer.Add(isoSel,1,WACV\|wx.EXPAND)
415	elemSizer.Add(wx.StaticText(General,label=' No. per cell'),0,WACV)
416	for elem in generalData['AtomTypes']:
417	numbTxt = wx.TextCtrl(General,value='%.1f'%(generalData['NoAtoms'][elem]),
418	style=wx.TE_READONLY)
419	numbTxt.SetBackgroundColour(VERY_LIGHT_GREY)
420	elemSizer.Add(numbTxt,0,WACV)
421	elemSizer.Add(wx.StaticText(General,label=' Atom weight'),0,WACV)
422	for wt in generalData['AtomMass']:
423	wtTxt = wx.TextCtrl(General,value='%.3f'%(wt),style=wx.TE_READONLY)
424	wtTxt.SetBackgroundColour(VERY_LIGHT_GREY)
425	elemSizer.Add(wtTxt,0,WACV)
426	elemSizer.Add(wx.StaticText(General,label=' Bond radii'),0,WACV)
427	for rad in generalData['BondRadii']:
428	bondRadii = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
429	bondRadii.SetBackgroundColour(VERY_LIGHT_GREY)
430	elemSizer.Add(bondRadii,0,WACV)
431	elemSizer.Add(wx.StaticText(General,label=' Angle radii'),0,WACV)
432	for rad in generalData['AngleRadii']:
433	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
434	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
435	elemSizer.Add(elemTxt,0,WACV)
436	elemSizer.Add(wx.StaticText(General,label=' van der Waals radii'),0,WACV)
437	for rad in generalData['vdWRadii']:
438	elemTxt = wx.TextCtrl(General,value='%.2f'%(rad),style=wx.TE_READONLY)
439	elemTxt.SetBackgroundColour(VERY_LIGHT_GREY)
440	elemSizer.Add(elemTxt,0,WACV)
441	elemSizer.Add(wx.StaticText(General,label=' Default color'),0,WACV)
442	for R,G,B in generalData['Color']:
443	colorTxt = wx.TextCtrl(General,value='',style=wx.TE_READONLY)
444	colorTxt.SetBackgroundColour(wx.Colour(R,G,B))
445	elemSizer.Add(colorTxt,0,WACV)
446	return elemSizer
447
448	def DenSizer():
449
450	mass = G2mth.getMass(generalData)
451	density,mattCoeff = G2mth.getDensity(generalData)
452	denSizer = wx.BoxSizer(wx.HORIZONTAL)
453	denSizer.Add(wx.StaticText(General,-1,' Density: '),0,WACV)
454	denTxt = wx.TextCtrl(General,-1,'%.3f'%(density),style=wx.TE_READONLY)
455	denTxt.SetBackgroundColour(VERY_LIGHT_GREY)
456	denSizer.Add(denTxt,0,WACV)
457	mattTxt = None
458	if generalData['Type'] == 'macromolecular' and mass > 0.0:
459	denSizer.Add(wx.StaticText(General,-1,' Matthews coeff.: '),
460	0,WACV)
461	mattTxt = wx.TextCtrl(General,-1,'%.3f'%(mattCoeff),style=wx.TE_READONLY)
462	mattTxt.SetBackgroundColour(VERY_LIGHT_GREY)
463	denSizer.Add(mattTxt,0,WACV)
464	return denSizer,denTxt,mattTxt
465
466	def PawleySizer():
467
468	def OnPawleyRef(event):
469	generalData['doPawley'] = pawlRef.GetValue()
470
471	def OnPawleyVal(event):
472	try:
473	dmin = float(pawlVal.GetValue())
474	if 0.25 <= dmin <= 20.:
475	generalData['Pawley dmin'] = dmin
476	except ValueError:
477	pass
478	pawlVal.SetValue("%.5f"%(generalData['Pawley dmin'])) #reset in case of error
479
480	def OnPawleyNegWt(event):
481	try:
482	wt = float(pawlNegWt.GetValue())
483	if 0. <= wt <= 1.:
484	generalData['Pawley neg wt'] = wt
485	except ValueError:
486	pass
487	pawlNegWt.SetValue("%.4f"%(generalData['Pawley neg wt'])) #reset in case of error
488
489	pawleySizer = wx.BoxSizer(wx.HORIZONTAL)
490	pawleySizer.Add(wx.StaticText(General,label=' Pawley controls: '),0,WACV)
491	pawlRef = wx.CheckBox(General,-1,label=' Do Pawley refinement?')
492	pawlRef.SetValue(generalData['doPawley'])
493	pawlRef.Bind(wx.EVT_CHECKBOX,OnPawleyRef)
494	pawleySizer.Add(pawlRef,0,WACV)
495	pawleySizer.Add(wx.StaticText(General,label=' Pawley dmin: '),0,WACV)
496	pawlVal = wx.TextCtrl(General,value='%.5f'%(generalData['Pawley dmin']),style=wx.TE_PROCESS_ENTER)
497	pawlVal.Bind(wx.EVT_TEXT_ENTER,OnPawleyVal)
498	pawlVal.Bind(wx.EVT_KILL_FOCUS,OnPawleyVal)
499	pawleySizer.Add(pawlVal,0,WACV)
500	pawleySizer.Add(wx.StaticText(General,label=' Pawley neg. wt.: '),0,WACV)
501	pawlNegWt = wx.TextCtrl(General,value='%.4f'%(generalData['Pawley neg wt']),style=wx.TE_PROCESS_ENTER)
502	pawlNegWt.Bind(wx.EVT_TEXT_ENTER,OnPawleyNegWt)
503	pawlNegWt.Bind(wx.EVT_KILL_FOCUS,OnPawleyNegWt)
504	pawleySizer.Add(pawlNegWt,0,WACV)
505	return pawleySizer
506
507	def MapSizer():
508
509	def OnMapType(event):
510	Map['MapType'] = mapType.GetValue()
511
512	def OnRefList(event):
513	Map['RefList'] = refList.GetValue()
514
515	def OnResVal(event):
516	try:
517	res = float(mapRes.GetValue())
518	if 0.25 <= res <= 20.:
519	Map['Resolution'] = res
520	except ValueError:
521	pass
522	mapRes.SetValue("%.2f"%(Map['Resolution'])) #reset in case of error
523
524	def OnCutOff(event):
525	try:
526	res = float(cutOff.GetValue())
527	if 10.0 <= res <= 100.:
528	Map['cutOff'] = res
529	except ValueError:
530	pass
531	cutOff.SetValue("%.1f"%(Map['cutOff'])) #reset in case of error
532
533	#patch
534	if 'cutOff' not in Map:
535	Map['cutOff'] = 100.0
536	mapTypes = ['Fobs','Fcalc','delt-F','2*Fo-Fc','Omit','2Fo-Fc Omit','Patterson']
537	refList = data['Histograms'].keys()
538	if not generalData['AtomTypes']:
539	mapTypes = ['Patterson',]
540	Map['MapType'] = 'Patterson'
541	mapSizer = wx.BoxSizer(wx.VERTICAL)
542	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
543	lineSizer.Add(wx.StaticText(General,label=' Fourier map controls: Map type: '),0,WACV)
544	mapType = wx.ComboBox(General,-1,value=Map['MapType'],choices=mapTypes,
545	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
546	mapType.Bind(wx.EVT_COMBOBOX,OnMapType)
547	lineSizer.Add(mapType,0,WACV)
548	lineSizer.Add(wx.StaticText(General,label=' Reflection set from: '),0,WACV)
549	refList = wx.ComboBox(General,-1,value=Map['RefList'],choices=refList,
550	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
551	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
552	lineSizer.Add(refList,0,WACV)
553	mapSizer.Add(lineSizer,0,WACV)
554	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
555	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
556	mapRes = wx.TextCtrl(General,value='%.2f'%(Map['Resolution']),style=wx.TE_PROCESS_ENTER)
557	mapRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
558	mapRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
559	line2Sizer.Add(mapRes,0,WACV)
560	line2Sizer.Add(wx.StaticText(General,label=' Peak cutoff %: '),0,WACV)
561	cutOff = wx.TextCtrl(General,value='%.1f'%(Map['cutOff']),style=wx.TE_PROCESS_ENTER)
562	cutOff.Bind(wx.EVT_TEXT_ENTER,OnCutOff)
563	cutOff.Bind(wx.EVT_KILL_FOCUS,OnCutOff)
564	line2Sizer.Add(cutOff,0,WACV)
565	mapSizer.Add(line2Sizer,0,WACV)
566	return mapSizer
567
568	def FlipSizer():
569	if 'k-Max' not in Flip: Flip['k-Max'] = 20.
570
571	def OnRefList(event):
572	Flip['RefList'] = refList.GetValue()
573
574	def OnNormElem(event):
575	PE = G2elemGUI.PickElement(G2frame,ifNone=True)
576	if PE.ShowModal() == wx.ID_OK:
577	Flip['Norm element'] = PE.Elem.strip()
578	normElem.SetLabel(Flip['Norm element'])
579	PE.Destroy()
580
581	def OnResVal(event):
582	try:
583	res = float(flipRes.GetValue())
584	if 0.25 <= res <= 20.:
585	Flip['Resolution'] = res
586	except ValueError:
587	pass
588	flipRes.SetValue("%.2f"%(Flip['Resolution'])) #reset in case of error
589
590	def OnkFactor(event):
591	try:
592	res = float(kFactor.GetValue())
593	if 0.1 <= res <= 1.2:
594	Flip['k-factor'] = res
595	except ValueError:
596	pass
597	kFactor.SetValue("%.3f"%(Flip['k-factor'])) #reset in case of error
598
599	def OnkMax(event):
600	try:
601	res = float(kMax.GetValue())
602	if res >= 10.:
603	Flip['k-Max'] = res
604	except ValueError:
605	pass
606	kMax.SetValue("%.1f"%(Flip['k-Max'])) #reset in case of error
607
608	refList = data['Histograms'].keys()
609	flipSizer = wx.BoxSizer(wx.VERTICAL)
610	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
611	lineSizer.Add(wx.StaticText(General,label=' Charge flip controls: Reflection set from: '),0,WACV)
612	refList = wx.ComboBox(General,-1,value=Flip['RefList'],choices=refList,
613	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
614	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
615	lineSizer.Add(refList,0,WACV)
616	lineSizer.Add(wx.StaticText(General,label=' Normalizing element: '),0,WACV)
617	normElem = wx.Button(General,label=Flip['Norm element'],style=wx.TE_READONLY)
618	normElem.Bind(wx.EVT_BUTTON,OnNormElem)
619	lineSizer.Add(normElem,0,WACV)
620	flipSizer.Add(lineSizer,0,WACV)
621	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
622	line2Sizer.Add(wx.StaticText(General,label=' Resolution: '),0,WACV)
623	flipRes = wx.TextCtrl(General,value='%.2f'%(Flip['Resolution']),style=wx.TE_PROCESS_ENTER)
624	flipRes.Bind(wx.EVT_TEXT_ENTER,OnResVal)
625	flipRes.Bind(wx.EVT_KILL_FOCUS,OnResVal)
626	line2Sizer.Add(flipRes,0,WACV)
627	line2Sizer.Add(wx.StaticText(General,label=' k-Factor (0.1-1.2): '),0,WACV)
628	kFactor = wx.TextCtrl(General,value='%.3f'%(Flip['k-factor']),style=wx.TE_PROCESS_ENTER)
629	kFactor.Bind(wx.EVT_TEXT_ENTER,OnkFactor)
630	kFactor.Bind(wx.EVT_KILL_FOCUS,OnkFactor)
631	line2Sizer.Add(kFactor,0,WACV)
632	line2Sizer.Add(wx.StaticText(General,label=' k-Max (>=10.0): '),0,WACV)
633	kMax = wx.TextCtrl(General,value='%.1f'%(Flip['k-Max']),style=wx.TE_PROCESS_ENTER)
634	kMax.Bind(wx.EVT_TEXT_ENTER,OnkMax)
635	kMax.Bind(wx.EVT_KILL_FOCUS,OnkMax)
636	line2Sizer.Add(kMax,0,WACV)
637	flipSizer.Add(line2Sizer,0,WACV)
638	return flipSizer
639
640	def MCSASizer():
641	Ind = {}
642
643	def OnRefList(event):
644	MCSAdata['Data source'] = refList.GetValue()
645
646	def OnDmin(event):
647	try:
648	val = float(dmin.GetValue())
649	if 1.0 <= val < 5.0:
650	MCSAdata['dmin'] = val
651	except ValueError:
652	pass
653	dmin.SetValue("%.3f"%(MCSAdata['dmin'])) #reset in case of error
654	MCSAdata['newDmin'] = True
655
656	def OnCycles(event):
657	MCSAdata['Cycles'] = int(cycles.GetValue())
658
659	def OnAlist(event):
660	MCSAdata['Algorithm'] = Alist.GetValue()
661	wx.CallAfter(UpdateGeneral)
662
663	def OnSlope(event):
664	try:
665	val = float(slope.GetValue())
666	if .25 <= val < 1.0:
667	MCSAdata['log slope'] = val
668	except ValueError:
669	pass
670	slope.SetValue("%.3f"%(MCSAdata['log slope'])) #reset in case of error
671
672	def OnAjump(event):
673	Obj = event.GetEventObject()
674	name,ind = Indx[Obj.GetId()]
675	try:
676	val = float(Obj.GetValue())
677	if .0 <= val <= 1.0:
678	MCSAdata[name][ind] = val
679	except ValueError:
680	pass
681	Obj.SetValue("%.3f"%(MCSAdata[name][ind]))
682
683	def OnRanStart(event):
684	MCSAdata['ranStart'] = ranStart.GetValue()
685
686	def OnAutoRan(event):
687	MCSAdata['autoRan'] = autoRan.GetValue()
688
689	def OnRanRange(event):
690	try:
691	val = float(ranRange.GetValue())/100
692	if 0.01 <= val <= 0.99:
693	MCSAdata['ranRange'] = val
694	except ValueError:
695	pass
696	ranRange.SetValue('%.1f'%(MCSAdata['ranRange']*100.))
697
698	def OnAnneal(event):
699	Obj = event.GetEventObject()
700	ind,fmt = Indx[Obj.GetId()]
701	if ind == 2: #No. trials
702	try:
703	val = int(Obj.GetValue())
704	if 1 <= val:
705	MCSAdata['Annealing'][ind] = val
706	except ValueError:
707	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
708	else:
709	try:
710	val = float(Obj.GetValue())
711	if .0 <= val:
712	MCSAdata['Annealing'][ind] = val
713	Obj.SetValue(fmt%(MCSAdata['Annealing'][ind]))
714	except ValueError:
715	MCSAdata['Annealing'][ind] = None
716	Obj.SetValue(str(MCSAdata['Annealing'][ind]))
717
718	refList = []
719	if len(data['Pawley ref']):
720	refList = ['Pawley reflections']
721	for item in data['Histograms'].keys():
722	if 'HKLF' in item or 'PWDR' in item:
723	refList.append(item)
724	mcsaSizer = wx.BoxSizer(wx.VERTICAL)
725	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
726	lineSizer.Add(wx.StaticText(General,label=' Monte Carlo/Simulated Annealing controls: Reflection set from: '),0,WACV)
727	refList = wx.ComboBox(General,-1,value=MCSAdata['Data source'],choices=refList,
728	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
729	refList.Bind(wx.EVT_COMBOBOX,OnRefList)
730	lineSizer.Add(refList,0,WACV)
731	lineSizer.Add(wx.StaticText(General,label=' d-min: '),0,WACV)
732	dmin = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['dmin']),style=wx.TE_PROCESS_ENTER)
733	dmin.Bind(wx.EVT_TEXT_ENTER,OnDmin)
734	dmin.Bind(wx.EVT_KILL_FOCUS,OnDmin)
735	lineSizer.Add(dmin,0,WACV)
736	mcsaSizer.Add(lineSizer)
737	mcsaSizer.Add((5,5),)
738	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
739	line2Sizer.Add(wx.StaticText(General,label=' MC/SA runs: '),0,WACV)
740	Cchoice = ['1','2','4','8','16','32','64','128','256']
741	cycles = wx.ComboBox(General,-1,value=str(MCSAdata.get('Cycles',1)),choices=Cchoice,
742	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
743	cycles.Bind(wx.EVT_COMBOBOX,OnCycles)
744	line2Sizer.Add(cycles,0,WACV)
745	line2Sizer.Add((5,0),)
746	ranStart = wx.CheckBox(General,-1,label=' MC/SA Refine at ')
747	ranStart.Bind(wx.EVT_CHECKBOX, OnRanStart)
748	ranStart.SetValue(MCSAdata.get('ranStart',False))
749	line2Sizer.Add(ranStart,0,WACV)
750	ranRange = wx.TextCtrl(General,-1,value='%.1f'%(MCSAdata.get('ranRange',0.10)*100),style=wx.TE_PROCESS_ENTER)
751	ranRange.Bind(wx.EVT_TEXT_ENTER,OnRanRange)
752	ranRange.Bind(wx.EVT_KILL_FOCUS,OnRanRange)
753	line2Sizer.Add(ranRange,0,WACV)
754	line2Sizer.Add(wx.StaticText(General,label='% of ranges. '),0,WACV)
755	# autoRan = wx.CheckBox(General,-1,label=' Do auto range reduction? ')
756	# autoRan.Bind(wx.EVT_CHECKBOX, OnAutoRan)
757	# autoRan.SetValue(MCSAdata.get('autoRan',False))
758	# line2Sizer.Add(autoRan,0,WACV)
759	mcsaSizer.Add(line2Sizer)
760	mcsaSizer.Add((5,5),)
761	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
762	Achoice = ['log','fast'] #these work
763	# Achoice = ['log','fast','cauchy','boltzmann']
764	line3Sizer.Add(wx.StaticText(General,label=' MC/SA schedule: '),0,WACV)
765	Alist = wx.ComboBox(General,-1,value=MCSAdata['Algorithm'],choices=Achoice,
766	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
767	Alist.Bind(wx.EVT_COMBOBOX,OnAlist)
768	line3Sizer.Add(Alist,0,WACV)
769	if MCSAdata['Algorithm'] in ['fast','boltzmann','cauchy']:
770	Names = [' A-jump: ',' B-jump: ']
771	parms = 'Jump coeff'
772	if MCSAdata['Algorithm'] in ['boltzmann','cauchy']:
773	Names = [' A-jump: ']
774	elif 'fast' in MCSAdata['Algorithm']:
775	Names = [' quench: ',' m-factor: ',' n-factor: ']
776	parms = 'fast parms'
777	for i,name in enumerate(Names):
778	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
779	Ajump = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata[parms][i]),style=wx.TE_PROCESS_ENTER)
780	Ajump.Bind(wx.EVT_TEXT_ENTER,OnAjump)
781	Ajump.Bind(wx.EVT_KILL_FOCUS,OnAjump)
782	Indx[Ajump.GetId()] = [parms,i]
783	line3Sizer.Add(Ajump,0,WACV)
784	elif 'log' in MCSAdata['Algorithm']:
785	line3Sizer.Add(wx.StaticText(General,label=' slope: '),0,WACV)
786	slope = wx.TextCtrl(General,-1,value='%.3f'%(MCSAdata['log slope']),style=wx.TE_PROCESS_ENTER)
787	slope.Bind(wx.EVT_TEXT_ENTER,OnSlope)
788	slope.Bind(wx.EVT_KILL_FOCUS,OnSlope)
789	line3Sizer.Add(slope,0,WACV)
790	mcsaSizer.Add(line3Sizer)
791	mcsaSizer.Add((5,5),)
792	line3Sizer = wx.BoxSizer(wx.HORIZONTAL)
793	line3Sizer.Add(wx.StaticText(General,label=' Annealing schedule: '),0,WACV)
794	names = [' Start temp: ',' Final temp: ',' No. trials: ']
795	fmts = ['%.1f','%.5f','%d']
796	for i,[name,fmt] in enumerate(zip(names,fmts)):
797	if MCSAdata['Annealing'][i]:
798	text = fmt%(MCSAdata['Annealing'][i])
799	else:
800	text = 'None'
801	line3Sizer.Add(wx.StaticText(General,label=name),0,WACV)
802	anneal = wx.TextCtrl(General,-1,value=text,style=wx.TE_PROCESS_ENTER)
803	anneal.Bind(wx.EVT_TEXT_ENTER,OnAnneal)
804	anneal.Bind(wx.EVT_KILL_FOCUS,OnAnneal)
805	Indx[anneal.GetId()] = [i,fmt]
806	line3Sizer.Add(anneal,0,WACV)
807	mcsaSizer.Add(line3Sizer)
808	return mcsaSizer
809
810	# UpdateGeneral execution continues here
811	if General.GetSizer():
812	General.GetSizer().Clear(True)
813	mainSizer = wx.BoxSizer(wx.VERTICAL)
814	mainSizer.Add((5,5),0)
815	mainSizer.Add(NameSizer(),0)
816	mainSizer.Add((5,5),0)
817	mainSizer.Add(CellSizer(),0)
818	mainSizer.Add((5,5),0)
819
820	Indx = {}
821	denSizer = None
822	if len(generalData['AtomTypes']):
823	denSizer = DenSizer()
824	mainSizer.Add(denSizer[0])
825	mainSizer.Add((5,5),0)
826	mainSizer.Add(ElemSizer())
827	G2gd.HorizontalLine(mainSizer,General)
828
829	mainSizer.Add(PawleySizer())
830	G2gd.HorizontalLine(mainSizer,General)
831
832	mainSizer.Add(MapSizer())
833	G2gd.HorizontalLine(mainSizer,General)
834
835	mainSizer.Add(FlipSizer())
836	G2gd.HorizontalLine(mainSizer,General)
837
838	mainSizer.Add(MCSASizer())
839	SetPhaseWindow(G2frame.dataFrame,General,mainSizer)
840	G2frame.dataFrame.SetStatusText('')
841
842	################################################################################
843	##### Atom routines
844	################################################################################
845
846	def FillAtomsGrid(Atoms):
847	'''Display the contents of the Atoms tab
848	'''
849	def RefreshAtomGrid(event):
850
851	r,c = event.GetRow(),event.GetCol()
852	if r < 0 and c < 0:
853	for row in range(Atoms.GetNumberRows()):
854	Atoms.SelectRow(row,True)
855	if r < 0: #double click on col label! Change all atoms!
856	sel = -1
857	noSkip = True
858	if Atoms.GetColLabelValue(c) == 'refine':
859	Type = generalData['Type']
860	if Type in ['nuclear','macromolecular']:
861	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
862	elif Type in ['magnetic',]:
863	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
864	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
865	if dlg.ShowModal() == wx.ID_OK:
866	sel = dlg.GetSelections()
867	parms = ''
868	for x in sel:
869	parms += choice[x][0]
870	dlg.Destroy()
871	elif Atoms.GetColLabelValue(c) == 'I/A':
872	choice = ['Isotropic','Anisotropic']
873	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal Motion',choice)
874	if dlg.ShowModal() == wx.ID_OK:
875	sel = dlg.GetSelection()
876	parms = choice[sel][0]
877	dlg.Destroy()
878	elif Atoms.GetColLabelValue(c) == 'Type':
879	choice = generalData['AtomTypes']
880	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom types',choice)
881	if dlg.ShowModal() == wx.ID_OK:
882	sel = dlg.GetSelection()
883	parms = choice[sel]
884	noSkip = False
885	Atoms.ClearSelection()
886	for row in range(Atoms.GetNumberRows()):
887	if parms == atomData[row][c]:
888	Atoms.SelectRow(row,True)
889	dlg.Destroy()
890	SetupGeneral()
891	elif Atoms.GetColLabelValue(c) == 'residue':
892	choice = []
893	for r in range(Atoms.GetNumberRows()):
894	if str(atomData[r][c]) not in choice:
895	choice.append(str(atomData[r][c]))
896	choice.sort()
897	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue',choice)
898	if dlg.ShowModal() == wx.ID_OK:
899	sel = dlg.GetSelection()
900	parms = choice[sel]
901	noSkip = False
902	Atoms.ClearSelection()
903	for row in range(Atoms.GetNumberRows()):
904	if parms == atomData[row][c]:
905	Atoms.SelectRow(row,True)
906	dlg.Destroy()
907	elif Atoms.GetColLabelValue(c) == 'res no':
908	choice = []
909	for r in range(Atoms.GetNumberRows()):
910	if str(atomData[r][c]) not in choice:
911	choice.append(str(atomData[r][c]))
912	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue no.',choice)
913	if dlg.ShowModal() == wx.ID_OK:
914	sel = dlg.GetSelection()
915	parms = choice[sel]
916	noSkip = False
917	Atoms.ClearSelection()
918	for row in range(Atoms.GetNumberRows()):
919	if int(parms) == atomData[row][c]:
920	Atoms.SelectRow(row,True)
921	dlg.Destroy()
922	elif Atoms.GetColLabelValue(c) == 'chain':
923	choice = []
924	for r in range(Atoms.GetNumberRows()):
925	if atomData[r][c] not in choice:
926	choice.append(atomData[r][c])
927	dlg = wx.SingleChoiceDialog(G2frame,'Select','Chain',choice)
928	if dlg.ShowModal() == wx.ID_OK:
929	sel = dlg.GetSelection()
930	parms = choice[sel]
931	noSkip = False
932	Atoms.ClearSelection()
933	for row in range(Atoms.GetNumberRows()):
934	if parms == atomData[row][c]:
935	Atoms.SelectRow(row,True)
936	dlg.Destroy()
937	elif Atoms.GetColLabelValue(c) == 'Uiso': #this needs to ask for value
938	pass #& then change all 'I' atoms
939	if sel >= 0 and noSkip:
940	ui = colLabels.index('U11')
941	us = colLabels.index('Uiso')
942	ss = colLabels.index('site sym')
943	for r in range(Atoms.GetNumberRows()):
944	ID = atomData[r][-1]
945	if parms != atomData[r][c] and Atoms.GetColLabelValue(c) == 'I/A':
946	if parms == 'A': #'I' --> 'A'
947	Uiso = float(Atoms.GetCellValue(r,us))
948	sytsym = atomData[r][ss]
949	CSI = G2spc.GetCSuinel(sytsym)
950	atomData[r][ui:ui+6] = Uiso*np.array(CSI[3])
951	atomData[r][us] = 0.0
952	Atoms.SetCellStyle(r,us,VERY_LIGHT_GREY,True)
953	for i in range(6):
954	ci = ui+i
955	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
956	if CSI[2][i]:
957	Atoms.SetCellStyle(r,ci,WHITE,False)
958	else: #'A' --> 'I'
959	Uij = atomData[r][ui:ui+6]
960	Uiso = (Uij[0]+Uij[1]+Uij[2])/3.0
961	atomData[r][us] = Uiso
962	Atoms.SetCellStyle(r,us,WHITE,False)
963	for i in range(6):
964	ci = ui+i
965	atomData[r][ci] = 0.0
966	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
967	if not Atoms.IsReadOnly(r,c):
968	if Atoms.GetColLabelValue(c) == 'refine':
969	rbExcl = rbAtmDict.get(atomData[r][-1],'')
970	if rbExcl:
971	for excl in rbExcl:
972	atomData[r][c] = parms.replace(excl,'')
973	else:
974	atomData[r][c] = parms
975	else:
976	atomData[r][c] = parms
977	if 'Atoms' in data['Drawing']:
978	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
979	wx.CallAfter(Paint)
980
981	def ChangeAtomCell(event):
982
983	def chkUij(Uij,CSI): #needs to do something!!!
984	return Uij
985
986	r,c = event.GetRow(),event.GetCol()
987	if r >= 0 and c >= 0:
988	ID = atomData[r][-1]
989	if Atoms.GetColLabelValue(c) in ['x','y','z']:
990	ci = colLabels.index('x')
991	XYZ = atomData[r][ci:ci+3]
992	if None in XYZ:
993	XYZ = [0,0,0]
994	SScol = colLabels.index('site sym')
995	Mulcol = colLabels.index('mult')
996	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
997	Sytsym,Mult = G2spc.SytSym(XYZ,SGData)
998	atomData[r][SScol] = Sytsym
999	atomData[r][Mulcol] = Mult
1000	if atomData[r][colLabels.index('I/A')] == 'A':
1001	ui = colLabels.index('U11')
1002	CSI = G2spc.GetCSuinel(Sytsym)
1003	atomData[r][ui:ui+6] = chkUij(atomData[r][ui:ui+6],Sytsym)
1004	for i in range(6):
1005	ci = i+ui
1006	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1007	if CSI[2][i]:
1008	Atoms.SetCellStyle(r,ci,WHITE,False)
1009	SetupGeneral()
1010	elif Atoms.GetColLabelValue(c) == 'I/A': #note use of text color to make it vanish!
1011	if atomData[r][c] == 'I':
1012	Uij = atomData[r][c+2:c+8]
1013	atomData[r][c+1] = (Uij[0]+Uij[1]+Uij[2])/3.0
1014	Atoms.SetCellStyle(r,c+1,WHITE,False)
1015	Atoms.SetCellTextColour(r,c+1,BLACK)
1016	for i in range(6):
1017	ci = i+colLabels.index('U11')
1018	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1019	Atoms.SetCellTextColour(r,ci,VERY_LIGHT_GREY)
1020	atomData[r][ci] = 0.0
1021	else:
1022	value = atomData[r][c+1]
1023	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1024	atomData[r][c+1] = 0.0
1025	Atoms.SetCellStyle(r,c+1,VERY_LIGHT_GREY,True)
1026	Atoms.SetCellTextColour(r,c+1,VERY_LIGHT_GREY)
1027	for i in range(6):
1028	ci = i+colLabels.index('U11')
1029	atomData[r][ci] = value*CSI[3][i]
1030	Atoms.SetCellStyle(r,ci,VERY_LIGHT_GREY,True)
1031	Atoms.SetCellTextColour(r,ci,BLACK)
1032	if CSI[2][i]:
1033	Atoms.SetCellStyle(r,ci,WHITE,False)
1034	elif Atoms.GetColLabelValue(c) in ['U11','U22','U33','U12','U13','U23']:
1035	value = atomData[r][c]
1036	CSI = G2spc.GetCSuinel(atomData[r][colLabels.index('site sym')])
1037	iUij = CSI[0][c-colLabels.index('U11')]
1038	for i in range(6):
1039	if iUij == CSI[0][i]:
1040	atomData[r][i+colLabels.index('U11')] = value*CSI[1][i]
1041	elif Atoms.GetColLabelValue(c) == 'refine':
1042	atomData[r][c] = atomData[r][c].replace(rbAtmDict.get(atomData[r][-1],''),'')
1043	if 'Atoms' in data['Drawing']:
1044	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1045	wx.CallAfter(Paint)
1046
1047	def AtomTypeSelect(event):
1048	r,c = event.GetRow(),event.GetCol()
1049	if Atoms.GetColLabelValue(c) == 'Type':
1050	PE = G2elemGUI.PickElement(G2frame)
1051	if PE.ShowModal() == wx.ID_OK:
1052	if PE.Elem != 'None':
1053	atomData[r][c] = PE.Elem.strip()
1054	name = atomData[r][c]
1055	if len(name) in [2,4]:
1056	atomData[r][c-1] = name[:2]+'(%d)'%(r+1)
1057	else:
1058	atomData[r][c-1] = name[:1]+'(%d)'%(r+1)
1059	PE.Destroy()
1060	SetupGeneral()
1061	wx.CallAfter(Paint)
1062	value = Atoms.GetCellValue(r,c)
1063	atomData[r][c] = value
1064	ID = atomData[r][-1]
1065	if 'Atoms' in data['Drawing']:
1066	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1067	SetupGeneral()
1068	else:
1069	event.Skip()
1070
1071	def RowSelect(event):
1072	r,c = event.GetRow(),event.GetCol()
1073	if not (event.AltDown() or (event.ShiftDown() and event.ControlDown())):
1074	Atoms.frm = -1
1075	G2frame.dataFrame.SetStatusText('')
1076	if r < 0 and c < 0:
1077	if Atoms.IsSelection():
1078	Atoms.ClearSelection()
1079	elif c < 0: #only row clicks
1080	if event.ControlDown() and not event.ShiftDown():
1081	if r in Atoms.GetSelectedRows():
1082	Atoms.DeselectRow(r)
1083	else:
1084	Atoms.SelectRow(r,True)
1085	elif event.ShiftDown() and not event.ControlDown():
1086	indxs = Atoms.GetSelectedRows()
1087	Atoms.ClearSelection()
1088	ibeg = 0
1089	if indxs:
1090	ibeg = indxs[-1]
1091	for row in range(ibeg,r+1):
1092	Atoms.SelectRow(row,True)
1093	elif event.AltDown() or (event.ShiftDown() and event.ControlDown()):
1094	if atomData[r][-1] in rbAtmDict:
1095	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be moved **')
1096	Atoms.frm = -1
1097	Atoms.ClearSelection()
1098	else:
1099	if Atoms.frm < 0: #pick atom to be moved
1100	Atoms.frm = r
1101	Atoms.SelectRow(r,True)
1102	n = colLabels.index('Name')
1103	G2frame.dataFrame.SetStatusText('Atom '+atomData[r][n]+' is to be moved')
1104	else: #move it
1105	item = atomData.pop(Atoms.frm)
1106	atomData.insert(r,item)
1107	Atoms.frm = -1
1108	G2frame.dataFrame.SetStatusText('')
1109	wx.CallAfter(Paint)
1110	else:
1111	Atoms.ClearSelection()
1112	Atoms.SelectRow(r,True)
1113
1114	def ChangeSelection(event):
1115	r,c = event.GetRow(),event.GetCol()
1116	if r < 0 and c < 0:
1117	Atoms.ClearSelection()
1118	if c < 0:
1119	if r in Atoms.GetSelectedRows():
1120	Atoms.DeselectRow(r)
1121	else:
1122	Atoms.SelectRow(r,True)
1123	if r < 0:
1124	if c in Atoms.GetSelectedCols():
1125	Atoms.DeselectCol(c)
1126	else:
1127	Atoms.SelectCol(c,True)
1128
1129	def Paint():
1130
1131	table = []
1132	rowLabels = []
1133	for i,atom in enumerate(atomData):
1134	table.append(atom)
1135	rowLabels.append(str(i))
1136	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
1137	Atoms.SetTable(atomTable, True)
1138	Atoms.frm = -1
1139	colType = colLabels.index('Type')
1140	colR = colLabels.index('refine')
1141	colSS = colLabels.index('site sym')
1142	colX = colLabels.index('x')
1143	colIA = colLabels.index('I/A')
1144	colU11 = colLabels.index('U11')
1145	colUiso = colLabels.index('Uiso')
1146	attr = wx.grid.GridCellAttr()
1147	attr.IncRef() #fix from Jim Hester
1148	attr.SetEditor(G2gd.GridFractionEditor(Atoms))
1149	for c in range(colX,colX+3):
1150	Atoms.SetColAttr(c, attr)
1151	for i in range(colU11-1,colU11+6):
1152	Atoms.SetColSize(i,50)
1153	for row in range(Atoms.GetNumberRows()):
1154	atId = atomData[row][-1]
1155	rbExcl = rbAtmDict.get(atId,'')
1156	Atoms.SetReadOnly(row,colSS,True) #site sym
1157	Atoms.SetReadOnly(row,colSS+1,True) #Mult
1158	if Atoms.GetCellValue(row,colIA) == 'A':
1159	CSI = G2spc.GetCSuinel(atomData[row][colLabels.index('site sym')])
1160	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1161	Atoms.SetCellTextColour(row,colUiso,VERY_LIGHT_GREY)
1162	for i in range(6):
1163	ci = colU11+i
1164	Atoms.SetCellTextColour(row,ci,BLACK)
1165	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1166	if CSI[2][i] and 'U' not in rbExcl:
1167	Atoms.SetCellStyle(row,ci,WHITE,False)
1168	else:
1169	Atoms.SetCellStyle(row,colUiso,WHITE,False)
1170	Atoms.SetCellTextColour(row,colUiso,BLACK)
1171	if 'U' in rbExcl:
1172	Atoms.SetCellStyle(row,colUiso,VERY_LIGHT_GREY,True)
1173	for i in range(6):
1174	ci = colU11+i
1175	Atoms.SetCellStyle(row,ci,VERY_LIGHT_GREY,True)
1176	Atoms.SetCellTextColour(row,ci,VERY_LIGHT_GREY)
1177	if 'X' in rbExcl:
1178	for c in range(0,colX+3):
1179	if c != colR:
1180	Atoms.SetCellStyle(row,c,VERY_LIGHT_GREY,True)
1181	Atoms.AutoSizeColumns(False)
1182
1183	# FillAtomsGrid executable code starts here
1184	generalData = data['General']
1185	atomData = data['Atoms']
1186	DData = data['Drawing']
1187	resRBData = data['RBModels'].get('Residue',[])
1188	vecRBData = data['RBModels'].get('Vector',[])
1189	rbAtmDict = {}
1190	for rbObj in resRBData+vecRBData:
1191	exclList = ['X' for i in range(len(rbObj['Ids']))]
1192	rbAtmDict.update(dict(zip(rbObj['Ids'],exclList)))
1193	if rbObj['ThermalMotion'][0] != 'None':
1194	for id in rbObj['Ids']:
1195	rbAtmDict[id] += 'U'
1196	# exclList will be 'x' or 'xu' if TLS used in RB
1197	Items = [G2gd.wxID_ATOMSEDITINSERT,G2gd.wxID_ATOMSEDITDELETE,G2gd.wxID_ATOMSREFINE,
1198	G2gd.wxID_ATOMSMODIFY,G2gd.wxID_ATOMSTRANSFORM,G2gd.wxID_ATOMVIEWINSERT,G2gd.wxID_ATOMMOVE]
1199	if atomData:
1200	for item in Items:
1201	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1202	else:
1203	for item in Items:
1204	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1205	Items = [G2gd.wxID_ATOMVIEWINSERT, G2gd.wxID_ATOMSVIEWADD,G2gd.wxID_ATOMMOVE]
1206	if 'showABC' in data['Drawing']:
1207	for item in Items:
1208	G2frame.dataFrame.AtomsMenu.Enable(item,True)
1209	else:
1210	for item in Items:
1211	G2frame.dataFrame.AtomsMenu.Enable(item,False)
1212
1213	AAchoice = ": ,ALA,ARG,ASN,ASP,CYS,GLN,GLU,GLY,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR,VAL,MSE,HOH,UNK"
1214	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,X,XU,U,F,FX,FXU,FU",]+ \
1215	3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_FLOAT+':10,4', #x,y,z,frac
1216	wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+":I,A",]
1217	Types += 7*[wg.GRID_VALUE_FLOAT+':10,5',]
1218	colLabels = ['Name','Type','refine','x','y','z','frac','site sym','mult','I/A','Uiso','U11','U22','U33','U12','U13','U23']
1219	if generalData['Type'] == 'magnetic':
1220	colLabels += ['Mx','My','Mz']
1221	Types[2] = wg.GRID_VALUE_CHOICE+": ,X,XU,U,M,MX,MXU,MU,F,FX,FXU,FU,FM,FMX,FMU,"
1222	Types += 3*[wg.GRID_VALUE_FLOAT+':10,4',]
1223	elif generalData['Type'] == 'macromolecular':
1224	colLabels = ['res no','residue','chain'] + colLabels
1225	Types = [wg.GRID_VALUE_STRING,
1226	wg.GRID_VALUE_CHOICE+AAchoice,
1227	wg.GRID_VALUE_STRING] + Types
1228	elif generalData['Type'] == 'modulated':
1229	Types += []
1230	colLabels += []
1231	SGData = data['General']['SGData']
1232	G2frame.dataFrame.SetStatusText('')
1233	if SGData['SGPolax']:
1234	G2frame.dataFrame.SetStatusText('Warning: The location of the origin is arbitrary in '+SGData['SGPolax'])
1235	Atoms.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeAtomCell)
1236	Atoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, AtomTypeSelect)
1237	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
1238	Atoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
1239	Atoms.Bind(wg.EVT_GRID_LABEL_RIGHT_CLICK, ChangeSelection)
1240	Atoms.SetMargins(0,0)
1241
1242	G2frame.dataFrame.setSizePosLeft([700,300])
1243	Paint()
1244
1245	def OnAtomAdd(event):
1246	AtomAdd(0,0,0)
1247	FillAtomsGrid(Atoms)
1248	event.StopPropagation()
1249	if data['Drawing']:
1250	G2plt.PlotStructure(G2frame,data)
1251
1252	def OnAtomViewAdd(event):
1253	try:
1254	drawData = data['Drawing']
1255	x,y,z = drawData['viewPoint'][0]
1256	AtomAdd(x,y,z)
1257	except:
1258	AtomAdd(0,0,0)
1259	FillAtomsGrid(Atoms)
1260	event.StopPropagation()
1261	G2plt.PlotStructure(G2frame,data)
1262
1263	def AtomAdd(x,y,z,El='H',Name='UNK'):
1264	atomData = data['Atoms']
1265	generalData = data['General']
1266	Ncol = Atoms.GetNumberCols()
1267	atId = ran.randint(0,sys.maxint)
1268	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1269	Sytsym,Mult = G2spc.SytSym([x,y,z],SGData)
1270	if generalData['Type'] == 'macromolecular':
1271	atomData.append([0,Name,'',Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1272	elif generalData['Type'] == 'nuclear':
1273	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1274	elif generalData['Type'] == 'magnetic':
1275	atomData.append([Name,El,'',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1276	SetupGeneral()
1277	if 'Atoms' in data['Drawing']:
1278	DrawAtomAdd(data['Drawing'],atomData[-1])
1279
1280	def OnAtomInsert(event):
1281	AtomInsert(0,0,0)
1282	FillAtomsGrid(Atoms)
1283	event.StopPropagation()
1284	G2plt.PlotStructure(G2frame,data)
1285
1286	def OnAtomViewInsert(event):
1287	if 'Drawing' in data:
1288	drawData = data['Drawing']
1289	x,y,z = drawData['viewPoint'][0]
1290	AtomAdd(x,y,z)
1291	FillAtomsGrid(Atoms)
1292	event.StopPropagation()
1293
1294	def OnAtomMove(event):
1295	drawData = data['Drawing']
1296	atomData = data['Atoms']
1297	x,y,z = drawData['viewPoint'][0]
1298	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1299	cx = colLabels.index('x')
1300	indx = Atoms.GetSelectedRows()
1301	if len(indx) != 1:
1302	print '** ERROR - only one atom can be moved **'
1303	elif atomData[indx[0]][-1] in rbAtmDict:
1304	print '** ERROR - Atoms in rigid bodies can not be moved **'
1305	else:
1306	atomData[indx[0]][cx:cx+3] = [x,y,z]
1307	SetupGeneral()
1308	FillAtomsGrid(Atoms)
1309	ID = atomData[indx[0]][-1]
1310	DrawAtomsReplaceByID(data['Drawing'],atomData[indx[0]],ID)
1311	G2plt.PlotStructure(G2frame,data)
1312	event.StopPropagation()
1313
1314	def DrawAtomsReplaceByID(drawingData,atom,ID):
1315	IDs = [ID,]
1316	atomData = drawingData['Atoms']
1317	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
1318	for ind in indx:
1319	atomData[ind] = MakeDrawAtom(atom,atomData[ind])
1320
1321	def MakeDrawAtom(atom,oldatom=None):
1322	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1323	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1324	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1325	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1326	generalData = data['General']
1327	SGData = generalData['SGData']
1328	if generalData['Type'] == 'nuclear':
1329	if oldatom:
1330	opr = oldatom[5]
1331	if atom[9] == 'A':
1332	X,U = G2spc.ApplyStringOps(opr,SGData,atom[3:6],atom[11:17])
1333	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:11]+list(U)+oldatom[17:]][0]
1334	else:
1335	X = G2spc.ApplyStringOps(opr,SGData,atom[3:6])
1336	atomInfo = [atom[:2]+list(X)+oldatom[5:9]+atom[9:]+oldatom[17:]][0]
1337	else:
1338	atomInfo = [atom[:2]+atom[3:6]+['1',]+['vdW balls',]+
1339	['',]+[[255,255,255],]+atom[9:]+[[],[]]][0]
1340	ct,cs = [1,8] #type & color
1341	elif generalData['Type'] == 'macromolecular':
1342	try:
1343	oneLetter = AA3letter.index(atom[1])
1344	except ValueError:
1345	oneLetter = -1
1346	atomInfo = [[atom[1].strip()+atom[0],]+
1347	[AA1letter[oneLetter]+atom[0],]+atom[2:5]+
1348	atom[6:9]+['1',]+['sticks',]+['',]+[[255,255,255],]+atom[12:]+[[],[]]][0]
1349	ct,cs = [4,11] #type & color
1350	elif generalData['Type'] == 'magnetic':
1351	if oldatom:
1352	atomInfo = [atom[:2]+oldatom[3:]][0]
1353	else:
1354	atomInfo = [atom[:2]+atom[3:6]+['vdW balls',]+['',]+atom[9:]+[[],[]]][0]
1355	ct,cs = [1,8] #type & color
1356	# elif generalData['Type'] == 'modulated':
1357	# ????? for future
1358	atNum = generalData['AtomTypes'].index(atom[ct])
1359	atomInfo[cs] = list(generalData['Color'][atNum])
1360	return atomInfo
1361
1362	def AtomInsert(x,y,z):
1363	indx = Atoms.GetSelectedRows()
1364	if indx:
1365	indx = indx[0]
1366	atomData = data['Atoms']
1367	generalData = data['General']
1368	Ncol = Atoms.GetNumberCols()
1369	E,SGData = G2spc.SpcGroup(generalData['SGData']['SpGrp'])
1370	Sytsym,Mult = G2spc.SytSym([0,0,0],SGData)
1371	atId = ran.randint(0,sys.maxint)
1372	if generalData['Type'] == 'macromolecular':
1373	atomData.insert(indx,[0,'UNK','','UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.10,0,0,0,0,0,0,atId])
1374	elif generalData['Type'] == 'nuclear':
1375	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,'I',0.01,0,0,0,0,0,0,atId])
1376	elif generalData['Type'] == 'magnetic':
1377	atomData.insert(indx,['UNK','UNK','',x,y,z,1,Sytsym,Mult,0,'I',0.01,0,0,0,0,0,0,0,0,0,atId])
1378	SetupGeneral()
1379
1380	def AtomDelete(event):
1381	indx = Atoms.GetSelectedRows()
1382	IDs = []
1383	if indx:
1384	atomData = data['Atoms']
1385	indx.reverse()
1386	for ind in indx:
1387	atom = atomData[ind]
1388	if atom[-1] in rbAtmDict:
1389	G2frame.dataFrame.SetStatusText('** ERROR - atom is in a rigid body and can not be deleted **')
1390	else:
1391	IDs.append(atom[-1])
1392	del atomData[ind]
1393	if 'Atoms' in data['Drawing']:
1394	DrawAtomsDeleteByIDs(IDs)
1395	wx.CallAfter(FillAtomsGrid,Atoms)
1396	G2plt.PlotStructure(G2frame,data)
1397	SetupGeneral()
1398	event.StopPropagation()
1399
1400	def AtomRefine(event):
1401	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1402	c = colLabels.index('refine')
1403	indx = Atoms.GetSelectedRows()
1404	if indx:
1405	atomData = data['Atoms']
1406	generalData = data['General']
1407	Type = generalData['Type']
1408	if Type in ['nuclear','macromolecular']:
1409	choice = ['F - site fraction','X - coordinates','U - thermal parameters']
1410	elif Type == 'magnetic':
1411	choice = ['F - site fraction','X - coordinates','U - thermal parameters','M - magnetic moment']
1412	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
1413	if dlg.ShowModal() == wx.ID_OK:
1414	sel = dlg.GetSelections()
1415	parms = ''
1416	for x in sel:
1417	parms += choice[x][0]
1418	for r in indx:
1419	if not Atoms.IsReadOnly(r,c):
1420	atomData[r][c] = parms
1421	Atoms.ForceRefresh()
1422	dlg.Destroy()
1423
1424	def AtomModify(event):
1425	indx = Atoms.GetSelectedRows()
1426	if indx:
1427	atomData = data['Atoms']
1428	generalData = data['General']
1429	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1430	choices = ['Type','Name','x','y','z','frac','I/A','Uiso']
1431	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom parameter',choices)
1432	parm = ''
1433	if dlg.ShowModal() == wx.ID_OK:
1434	sel = dlg.GetSelection()
1435	parm = choices[sel]
1436	cid = colLabels.index(parm)
1437	dlg.Destroy()
1438	if parm in ['Type']:
1439	dlg = G2elemGUI.PickElement(G2frame)
1440	if dlg.ShowModal() == wx.ID_OK:
1441	if dlg.Elem not in ['None']:
1442	El = dlg.Elem.strip()
1443	for r in indx:
1444	if not Atoms.IsReadOnly(r,cid):
1445	atomData[r][cid] = El
1446	if len(El) in [2,4]:
1447	atomData[r][cid-1] = El[:2]+'(%d)'%(r+1)
1448	else:
1449	atomData[r][cid-1] = El[:1]+'(%d)'%(r+1)
1450	SetupGeneral()
1451	if 'Atoms' in data['Drawing']:
1452	for r in indx:
1453	ID = atomData[r][-1]
1454	DrawAtomsReplaceByID(data['Drawing'],atomData[r],ID)
1455	FillAtomsGrid(Atoms)
1456	dlg.Destroy()
1457	elif parm in ['Name',]:
1458	dlg = wx.MessageDialog(G2frame,'Do you really want to rename the selected atoms?','Rename',
1459	wx.YES_NO \| wx.ICON_QUESTION)
1460	try:
1461	result = dlg.ShowModal()
1462	if result == wx.ID_YES:
1463	for r in indx:
1464	if not Atoms.IsReadOnly(r,cid+1):
1465	El = atomData[r][cid+1]
1466	if len(El) in [2,4]:
1467	atomData[r][cid] = El[:2]+'(%d)'%(r+1)
1468	else:
1469	atomData[r][cid] = El[:1]+'(%d)'%(r+1)
1470	FillAtomsGrid(Atoms)
1471	finally:
1472	dlg.Destroy()
1473
1474	elif parm in ['I/A']:
1475	choices = ['Isotropic','Anisotropic']
1476	dlg = wx.SingleChoiceDialog(G2frame,'Select','Thermal parameter model',choices)
1477	if dlg.ShowModal() == wx.ID_OK:
1478	sel = dlg.GetSelection()
1479	parm = choices[sel][0]
1480	for r in indx:
1481	if not Atoms.IsReadOnly(r,cid):
1482	atomData[r][cid] = parm
1483	FillAtomsGrid(Atoms)
1484	dlg.Destroy()
1485	elif parm in ['frac','Uiso']:
1486	limits = [0.,1.]
1487	val = 1.0
1488	if parm in ['Uiso']:
1489	limits = [0.,0.25]
1490	val = 0.01
1491	dlg = G2gd.SingleFloatDialog(G2frame,'New value','Enter new value for '+parm,val,limits)
1492	if dlg.ShowModal() == wx.ID_OK:
1493	parm = dlg.GetValue()
1494	for r in indx:
1495	if not Atoms.IsReadOnly(r,cid):
1496	atomData[r][cid] = parm
1497	SetupGeneral()
1498	FillAtomsGrid(Atoms)
1499	dlg.Destroy()
1500	elif parm in ['x','y','z']:
1501	limits = [-1.,1.]
1502	val = 0.
1503	dlg = G2gd.SingleFloatDialog(G2frame,'Atom shift','Enter shift for '+parm,val,limits)
1504	if dlg.ShowModal() == wx.ID_OK:
1505	parm = dlg.GetValue()
1506	for r in indx:
1507	if not Atoms.IsReadOnly(r,cid):
1508	atomData[r][cid] += parm
1509	SetupGeneral()
1510	FillAtomsGrid(Atoms)
1511	dlg.Destroy()
1512
1513	def AtomTransform(event):
1514	indx = Atoms.GetSelectedRows()
1515	if indx:
1516	generalData = data['General']
1517	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1518	cx = colLabels.index('x')
1519	cuia = colLabels.index('I/A')
1520	cuij = colLabels.index('U11')
1521	css = colLabels.index('site sym')
1522	atomData = data['Atoms']
1523	generalData = data['General']
1524	SGData = generalData['SGData']
1525	dlg = G2gd.SymOpDialog(G2frame,SGData,True,True)
1526	New = False
1527	try:
1528	if dlg.ShowModal() == wx.ID_OK:
1529	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
1530	Cell = np.array(Cell)
1531	cent = SGData['SGCen'][Cent]
1532	M,T = SGData['SGOps'][Opr]
1533	for ind in indx:
1534	XYZ = np.array(atomData[ind][cx:cx+3])
1535	XYZ = np.inner(M,XYZ)+T
1536	if Inv:
1537	XYZ = -XYZ
1538	XYZ = XYZ+cent+Cell
1539	if Force:
1540	XYZ = G2spc.MoveToUnitCell(XYZ)
1541	if New:
1542	atom = copy.copy(atomData[ind])
1543	else:
1544	atom = atomData[ind]
1545	atom[cx:cx+3] = XYZ
1546	atom[css:css+2] = G2spc.SytSym(XYZ,SGData)
1547	if atom[cuia] == 'A':
1548	Uij = atom[cuij:cuij+6]
1549	U = G2spc.Uij2U(Uij)
1550	U = np.inner(np.inner(M,U),M)
1551	Uij = G2spc.U2Uij(U)
1552	atom[cuij:cuij+6] = Uij
1553	if New:
1554	atomData.append(atom)
1555	finally:
1556	dlg.Destroy()
1557	Atoms.ClearSelection()
1558	if New:
1559	FillAtomsGrid(Atoms)
1560	else:
1561	Atoms.ForceRefresh()
1562
1563	def OnDistAnglePrt(event):
1564	'save distances and angles to a file'
1565	fp = file(os.path.abspath(os.path.splitext(G2frame.GSASprojectfile
1566	)[0]+'.disagl'),'w')
1567	OnDistAngle(event,fp=fp)
1568	fp.close()
1569
1570	def OnDistAngle(event,fp=None):
1571	'Compute distances and angles'
1572	indx = Atoms.GetSelectedRows()
1573	Oxyz = []
1574	xyz = []
1575	DisAglData = {}
1576	DisAglCtls = {}
1577	if indx:
1578	generalData = data['General']
1579	DisAglData['OrigIndx'] = indx
1580	if 'DisAglCtls' in generalData:
1581	DisAglCtls = generalData['DisAglCtls']
1582	dlg = G2gd.DisAglDialog(G2frame,DisAglCtls,generalData)
1583	if dlg.ShowModal() == wx.ID_OK:
1584	DisAglCtls = dlg.GetData()
1585	else:
1586	dlg.Destroy()
1587	return
1588	dlg.Destroy()
1589	generalData['DisAglCtls'] = DisAglCtls
1590	atomData = data['Atoms']
1591	colLabels = [Atoms.GetColLabelValue(c) for c in range(Atoms.GetNumberCols())]
1592	cx = colLabels.index('x')
1593	cn = colLabels.index('Name')
1594	for i,atom in enumerate(atomData):
1595	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1596	if i in indx:
1597	Oxyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1598	DisAglData['OrigAtoms'] = Oxyz
1599	DisAglData['TargAtoms'] = xyz
1600	generalData = data['General']
1601	DisAglData['SGData'] = generalData['SGData']
1602	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1603	if 'pId' in data:
1604	DisAglData['pId'] = data['pId']
1605	DisAglData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
1606	try:
1607	if fp:
1608	G2stMn.PrintDistAngle(DisAglCtls,DisAglData,fp)
1609	else:
1610	G2stMn.PrintDistAngle(DisAglCtls,DisAglData)
1611	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1612	G2frame.ErrorDialog('Distance/Angle calculation','try again but do "Reset" to fill in missing atom types')
1613	else:
1614	print "select one or more rows of atoms"
1615	G2frame.ErrorDialog('Select atom',"select one or more rows of atoms then redo")
1616
1617	def OnIsoDistortCalc(event):
1618	'''Compute the ISODISTORT mode values from the current coordinates.
1619	Called in response to the (Phase/Atoms tab) AtomCompute
1620	"Compute ISODISTORT mode values" menu item, which should be enabled
1621	only when Phase['ISODISTORT'] is defined.
1622	'''
1623	def _onClose(event):
1624	dlg.EndModal(wx.ID_CANCEL)
1625	def fmtHelp(item,fullname):
1626	helptext = "A new variable"
1627	if item[-3]:
1628	helptext += " named "+str(item[-3])
1629	helptext += " is a linear combination of the following parameters:\n"
1630	first = True
1631	for term in item[:-3]:
1632	line = ''
1633	var = str(term[1])
1634	m = term[0]
1635	if first:
1636	first = False
1637	line += ' = '
1638	else:
1639	if m >= 0:
1640	line += ' + '
1641	else:
1642	line += ' - '
1643	m = abs(m)
1644	line += '%.3f*%s '%(m,var)
1645	varMean = G2obj.fmtVarDescr(var)
1646	helptext += "\n" + line + " ("+ varMean + ")"
1647	helptext += '\n\nISODISTORT full name: '+str(fullname)
1648	return helptext
1649
1650	if 'ISODISTORT' not in data:
1651	raise Exception,"Should not happen: 'ISODISTORT' not in data"
1652	if len(data.get('Histograms',[])) == 0:
1653	G2frame.ErrorDialog(
1654	'No data',
1655	'Sorry, this computation requires that a histogram first be added to the phase'
1656	)
1657	return
1658	Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint
1659	# make a lookup table for constraints
1660	sub = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Constraints')
1661	Constraints = G2frame.PatternTree.GetItemPyData(sub)
1662	constDict = {}
1663	for item in Constraints:
1664	if item.startswith('_'): continue
1665	for c in Constraints[item]:
1666	if c[-1] != 'f' or not c[-3]: continue
1667	constDict[c[-3]] = c
1668
1669	ISO = data['ISODISTORT']
1670	parmDict,varyList = G2frame.MakeLSParmDict()
1671
1672	dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400),
1673	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER)
1674	mainSizer = wx.BoxSizer(wx.VERTICAL)
1675	mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
1676	'ISODISTORT mode computation for cordinates in phase '+
1677	str(data['General'].get('Name'))))
1678	aSizer = wx.BoxSizer(wx.HORIZONTAL)
1679	panel1 = wxscroll.ScrolledPanel(
1680	dlg, wx.ID_ANY,#size=(100,200),
1681	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1682	subSizer1 = wx.FlexGridSizer(cols=2,hgap=5,vgap=2)
1683	panel2 = wxscroll.ScrolledPanel(
1684	dlg, wx.ID_ANY,#size=(100,200),
1685	style = wx.TAB_TRAVERSAL\|wx.SUNKEN_BORDER)
1686	subSizer2 = wx.FlexGridSizer(cols=3,hgap=5,vgap=2)
1687	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name '))
1688	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1689	subSizer2.Add((-1,-1))
1690	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name '))
1691	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
1692
1693	if 'G2VarList' in ISO:
1694	deltaList = []
1695	for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']):
1696	dvar = gv.varname()
1697	var = dvar.replace('::dA','::A')
1698	albl = Ilbl[:Ilbl.rfind('_')]
1699	v = Ilbl[Ilbl.rfind('_')+1:]
1700	pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)]
1701	if var in parmDict:
1702	cval = parmDict[var][0]
1703	else:
1704	dlg.EndModal(wx.ID_CANCEL)
1705	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1706	return
1707	deltaList.append(cval-pval)
1708	modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList)
1709	for lbl,xyz,var,val,G2var in zip(ISO['IsoVarList'],deltaList,
1710	ISO['IsoModeList'],modeVals,ISO['G2ModeList']):
1711	if G2var in constDict:
1712	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1713	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1714	else:
1715	subSizer2.Add((-1,-1))
1716	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1717	try:
1718	value = G2py3.FormatSigFigs(xyz)
1719	except TypeError:
1720	value = str(xyz)
1721	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1722	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1723	try:
1724	value = G2py3.FormatSigFigs(val)
1725	except TypeError:
1726	value = str(val)
1727	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1728	if 'G2OccVarList' in ISO:
1729	deltaList = []
1730	for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']):
1731	var = gv.varname()
1732	albl = Ilbl[:Ilbl.rfind('_')]
1733	#v = Ilbl[Ilbl.rfind('_')+1:]
1734	pval = ISO['BaseOcc'][albl]
1735	if var in parmDict:
1736	cval = parmDict[var][0]
1737	else:
1738	dlg.EndModal(wx.ID_CANCEL)
1739	G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var))
1740	return
1741	deltaList.append(cval-pval)
1742	modeVals = np.inner(ISO['Var2OccMatrix'],deltaList)
1743	for lbl,xyz,var,val,G2var in zip(ISO['OccVarList'],deltaList,
1744	ISO['OccModeList'],modeVals,ISO['G2OccModeList']):
1745	if G2var in constDict:
1746	ch = G2gd.HelpButton(panel2,fmtHelp(constDict[G2var],var))
1747	subSizer2.Add(ch,0,wx.LEFT\|wx.RIGHT\|WACV\|wx.ALIGN_CENTER,1)
1748	else:
1749	subSizer2.Add((-1,-1))
1750	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)))
1751	try:
1752	value = G2py3.FormatSigFigs(xyz)
1753	except TypeError:
1754	value = str(xyz)
1755	subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1756	#subSizer.Add((10,-1))
1757	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var)))
1758	try:
1759	value = G2py3.FormatSigFigs(val)
1760	except TypeError:
1761	value = str(val)
1762	subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT)
1763
1764	# finish up ScrolledPanel
1765	panel1.SetSizer(subSizer1)
1766	panel2.SetSizer(subSizer2)
1767	panel1.SetAutoLayout(1)
1768	panel1.SetupScrolling()
1769	panel2.SetAutoLayout(1)
1770	panel2.SetupScrolling()
1771	# Allow window to be enlarged but not made smaller
1772	dlg.SetSizer(mainSizer)
1773	w1,l1 = subSizer1.GetSize()
1774	w2,l2 = subSizer2.GetSize()
1775	panel1.SetMinSize((w1+10,200))
1776	panel2.SetMinSize((w2+20,200))
1777	aSizer.Add(panel1,1, wx.ALL\|wx.EXPAND,1)
1778	aSizer.Add(panel2,2, wx.ALL\|wx.EXPAND,1)
1779	mainSizer.Add(aSizer,1, wx.ALL\|wx.EXPAND,1)
1780
1781	# make OK button
1782	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
1783	btn = wx.Button(dlg, wx.ID_CLOSE)
1784	btn.Bind(wx.EVT_BUTTON,_onClose)
1785	btnsizer.Add(btn)
1786	mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1787
1788	mainSizer.Fit(dlg)
1789	dlg.SetMinSize(dlg.GetSize())
1790	dlg.ShowModal()
1791	dlg.Destroy()
1792
1793	def OnReImport(event):
1794	generalData = data['General']
1795	cx,ct,cs,cia = generalData['AtomPtrs']
1796	reqrdr = G2frame.dataFrame.ReImportMenuId.get(event.GetId())
1797	rdlist = G2frame.OnImportGeneric(reqrdr,
1798	G2frame.ImportPhaseReaderlist,'phase')
1799	if len(rdlist) == 0: return
1800	# rdlist is only expected to have one element
1801	rd = rdlist[0]
1802	G2frame.OnFileSave(event)
1803	# rd contains all info for a phase
1804	PhaseName = rd.Phase['General']['Name']
1805	print 'Read phase '+str(PhaseName)+' from file '+str(G2frame.lastimport)
1806	atomData = data['Atoms']
1807	atomNames = []
1808	for atom in atomData:
1809	atomNames.append(atom[:ct+1])
1810	for atom in rd.Phase['Atoms']:
1811	try:
1812	idx = atomNames.index(atom[:ct+1])
1813	atomData[idx][:-1] = atom[:-1]
1814	except ValueError:
1815	print atom[:ct+1], 'not in Atom array; not updated'
1816	wx.CallAfter(FillAtomsGrid,Atoms)
1817
1818
1819	################################################################################
1820	#Structure drawing GUI stuff
1821	################################################################################
1822
1823	def SetupDrawingData():
1824	generalData = data['General']
1825	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1826	atomData = data['Atoms']
1827	AA3letter = ['ALA','ARG','ASN','ASP','CYS','GLN','GLU','GLY','HIS','ILE',
1828	'LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','MSE','HOH','WAT','UNK']
1829	AA1letter = ['A','R','N','D','C','Q','E','G','H','I',
1830	'L','K','M','F','P','S','T','W','Y','V','M',' ',' ',' ']
1831	defaultDrawing = {'Atoms':[],'viewPoint':[[0.5,0.5,0.5],[]],'showHydrogen':True,
1832	'backColor':[0,0,0],'depthFog':False,'Zclip':50.0,'cameraPos':50.,'Zstep':0.5,
1833	'radiusFactor':0.85,'contourLevel':1.,'bondRadius':0.1,'ballScale':0.33,
1834	'vdwScale':0.67,'ellipseProb':50,'sizeH':0.50,'unitCellBox':True,
1835	'showABC':True,'selectedAtoms':[],'Atoms':[],'oldxy':[],
1836	'bondList':{},'viewDir':[1,0,0]}
1837	V0 = np.array([0,0,1])
1838	V = np.inner(Amat,V0)
1839	V /= np.sqrt(np.sum(V**2))
1840	A = np.arccos(np.sum(V*V0))
1841	defaultDrawing['Quaternion'] = G2mth.AV2Q(A,[0,1,0])
1842	try:
1843	drawingData = data['Drawing']
1844	except KeyError:
1845	data['Drawing'] = {}
1846	drawingData = data['Drawing']
1847	if not drawingData: #fill with defaults if empty
1848	drawingData.update(defaultDrawing)
1849	if 'Zstep' not in drawingData:
1850	drawingData['Zstep'] = 0.5
1851	if 'contourLevel' not in drawingData:
1852	drawingData['contourLevel'] = 1.
1853	if 'viewDir' not in drawingData:
1854	drawingData['viewDir'] = [0,0,1]
1855	if 'Quaternion' not in drawingData:
1856	drawingData['Quaternion'] = G2mth.AV2Q(2*np.pi,np.inner(Amat,[0,0,1]))
1857	if 'showRigidBodies' not in drawingData:
1858	drawingData['showRigidBodies'] = True
1859	cx,ct,cs,ci = [0,0,0,0]
1860	if generalData['Type'] == 'nuclear':
1861	cx,ct,cs,ci = [2,1,6,17] #x, type, style & index
1862	elif generalData['Type'] == 'macromolecular':
1863	cx,ct,cs,ci = [5,4,9,20] #x, type, style & index
1864	elif generalData['Type'] == 'magnetic':
1865	cx,ct,cs,ci = [2,1,6,20] #x, type, style & index
1866	# elif generalData['Type'] == 'modulated':
1867	# ????? for future
1868	drawingData['atomPtrs'] = [cx,ct,cs,ci]
1869	if not drawingData.get('Atoms'):
1870	for atom in atomData:
1871	DrawAtomAdd(drawingData,atom)
1872	data['Drawing'] = drawingData
1873
1874	def DrawAtomAdd(drawingData,atom):
1875	drawingData['Atoms'].append(MakeDrawAtom(atom))
1876
1877	def OnRestraint(event):
1878	indx = drawAtoms.GetSelectedRows()
1879	restData = G2frame.PatternTree.GetItemPyData(
1880	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'))
1881	drawingData = data['Drawing']
1882	generalData = data['General']
1883	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1884	cx,ct,cs,ci = drawingData['atomPtrs']
1885	atomData = drawingData['Atoms']
1886	atNames = []
1887	atXYZ = []
1888	atSymOp = []
1889	atIndx = []
1890	for item in indx:
1891	atXYZ.append(np.array(atomData[item][cx:cx+3]))
1892	atSymOp.append(atomData[item][cs-1])
1893	atIndx.append(atomData[item][ci])
1894	if event.GetId() == G2gd.wxID_DRAWRESTRBOND and len(indx) == 2:
1895	try:
1896	bondData = restData[PhaseName]['Bond']
1897	except KeyError:
1898	bondData = {'wtFactor':1.0,'Bonds':[],'Use':True}
1899	restData[PhaseName] = {}
1900	restData[PhaseName]['Bond'] = bondData
1901	dist = G2mth.getRestDist(atXYZ,Amat)
1902	bondData['Bonds'].append([atIndx,atSymOp,1.54,0.01])
1903	elif event.GetId() == G2gd.wxID_DRAWRESTRANGLE and len(indx) == 3:
1904	try:
1905	angleData = restData[PhaseName]['Angle']
1906	except KeyError:
1907	angleData = {'wtFactor':1.0,'Angles':[],'Use':True}
1908	restData[PhaseName] = {}
1909	restData[PhaseName]['Angle'] = angleData
1910	angle = G2mth.getRestAngle(atXYZ,Amat)
1911	angleData['Angles'].append([atIndx,atSymOp,109.5,1.0])
1912	elif event.GetId() == G2gd.wxID_DRAWRESTRPLANE and len(indx) > 3:
1913	try:
1914	planeData = restData[PhaseName]['Plane']
1915	except KeyError:
1916	planeData = {'wtFactor':1.0,'Planes':[],'Use':True}
1917	restData[PhaseName] = {}
1918	restData[PhaseName]['Plane'] = planeData
1919	plane = G2mth.getRestPlane(atXYZ,Amat)
1920	planeData['Planes'].append([atIndx,atSymOp,0.0,0.01])
1921	elif event.GetId() == G2gd.wxID_DRAWRESTRCHIRAL and len(indx) == 4:
1922	try:
1923	chiralData = restData[PhaseName]['Chiral']
1924	except KeyError:
1925	chiralData = {'wtFactor':1.0,'Volumes':[],'Use':True}
1926	restData[PhaseName] = {}
1927	restData[PhaseName]['Chiral'] = chiralData
1928	volume = G2mth.getRestChiral(atXYZ,Amat)
1929	chiralData['Volumes'].append([atIndx,atSymOp,2.5,0.1])
1930	else:
1931	print '**** ERROR wrong number of atoms selected for this restraint'
1932	return
1933	G2frame.PatternTree.SetItemPyData(
1934	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Restraints'),restData)
1935
1936	def OnDefineRB(event):
1937	indx = drawAtoms.GetSelectedRows()
1938	indx.sort()
1939	RBData = G2frame.PatternTree.GetItemPyData(
1940	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
1941	drawingData = data['Drawing']
1942	generalData = data['General']
1943	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
1944	cx,ct,cs,ci = drawingData['atomPtrs']
1945	atomData = drawingData['Atoms']
1946	rbXYZ = []
1947	rbType = []
1948	atNames = []
1949	AtInfo = RBData['Residue']['AtInfo']
1950	for i,item in enumerate(indx):
1951	rbtype = atomData[item][ct]
1952	atNames.append(rbtype+str(i))
1953	rbType.append(rbtype)
1954	if rbtype not in AtInfo:
1955	Info = G2elem.GetAtomInfo(rbtype)
1956	AtInfo[rbtype] = [Info['Drad'],Info['Color']]
1957	rbXYZ.append(np.inner(np.array(atomData[item][cx:cx+3]),Amat))
1958	rbXYZ = np.array(rbXYZ)
1959	rbXYZ -= rbXYZ[0]
1960	rbId = ran.randint(0,sys.maxint)
1961	rbName = 'UNKRB'
1962	dlg = wx.TextEntryDialog(G2frame,'Enter the name for the new rigid body',
1963	'Edit rigid body name',rbName ,style=wx.OK)
1964	if dlg.ShowModal() == wx.ID_OK:
1965	rbName = dlg.GetValue()
1966	dlg.Destroy()
1967	RBData['Residue'][rbId] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbType,
1968	'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0}
1969	RBData['RBIds']['Residue'].append(rbId)
1970	G2frame.dataFrame.SetStatusText('New rigid body UNKRB added to set of Residue rigid bodies')
1971
1972	################################################################################
1973	##### Atom draw routines
1974	################################################################################
1975
1976	def UpdateDrawAtoms(atomStyle=''):
1977	def RefreshAtomGrid(event):
1978	def SetChoice(name,c,n=0):
1979	choice = []
1980	for r in range(len(atomData)):
1981	if n:
1982	srchStr = str(atomData[r][c][:n])
1983	else:
1984	srchStr = str(atomData[r][c])
1985	if srchStr not in choice:
1986	if n:
1987	choice.append(str(atomData[r][c][:n]))
1988	else:
1989	choice.append(str(atomData[r][c]))
1990	choice.sort()
1991
1992	dlg = wx.MultiChoiceDialog(G2frame,'Select',name,choice)
1993	if dlg.ShowModal() == wx.ID_OK:
1994	sel = dlg.GetSelections()
1995	parms = []
1996	for x in sel:
1997	parms.append(choice[x])
1998	noSkip = False
1999	drawAtoms.ClearSelection()
2000	drawingData['selectedAtoms'] = []
2001	for row in range(len(atomData)):
2002	test = atomData[row][c]
2003	if n:
2004	test = test[:n]
2005	if test in parms:
2006	drawAtoms.SelectRow(row,True)
2007	drawingData['selectedAtoms'].append(row)
2008	G2plt.PlotStructure(G2frame,data)
2009	dlg.Destroy()
2010
2011	r,c = event.GetRow(),event.GetCol()
2012	if r < 0 and c < 0:
2013	for row in range(drawAtoms.GetNumberRows()):
2014	drawingData['selectedAtoms'].append(row)
2015	drawAtoms.SelectRow(row,True)
2016	elif r < 0: #dclick on col label
2017	sel = -1
2018	Parms = False
2019	noSkip = True
2020	if drawAtoms.GetColLabelValue(c) == 'Style':
2021	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2022	if dlg.ShowModal() == wx.ID_OK:
2023	sel = dlg.GetSelection()
2024	parms = styleChoice[sel]
2025	for r in range(len(atomData)):
2026	atomData[r][c] = parms
2027	drawAtoms.SetCellValue(r,c,parms)
2028	FindBondsDraw()
2029	G2plt.PlotStructure(G2frame,data)
2030	dlg.Destroy()
2031	elif drawAtoms.GetColLabelValue(c) == 'Label':
2032	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom labelling style',labelChoice)
2033	if dlg.ShowModal() == wx.ID_OK:
2034	sel = dlg.GetSelection()
2035	parms = labelChoice[sel]
2036	for r in range(len(atomData)):
2037	atomData[r][c] = parms
2038	drawAtoms.SetCellValue(r,c,parms)
2039	dlg.Destroy()
2040	elif drawAtoms.GetColLabelValue(c) == 'Color':
2041	dlg = wx.ColourDialog(G2frame)
2042	if dlg.ShowModal() == wx.ID_OK:
2043	color = dlg.GetColourData().GetColour()
2044	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2045	attr.SetReadOnly(True)
2046	attr.SetBackgroundColour(color)
2047	for r in range(len(atomData)):
2048	atomData[r][c] = color
2049	drawingData['Atoms'][r][c] = color
2050	drawAtoms.SetAttr(r,c,attr)
2051	UpdateDrawAtoms()
2052	dlg.Destroy()
2053	elif drawAtoms.GetColLabelValue(c) == 'Residue':
2054	SetChoice('Residue',c,3)
2055	elif drawAtoms.GetColLabelValue(c) == '1-letter':
2056	SetChoice('1-letter',c,1)
2057	elif drawAtoms.GetColLabelValue(c) == 'Chain':
2058	SetChoice('Chain',c)
2059	elif drawAtoms.GetColLabelValue(c) == 'Name':
2060	SetChoice('Name',c)
2061	elif drawAtoms.GetColLabelValue(c) == 'Sym Op':
2062	SetChoice('Name',c)
2063	elif drawAtoms.GetColLabelValue(c) == 'Type':
2064	SetChoice('Type',c)
2065	elif drawAtoms.GetColLabelValue(c) in ['x','y','z','I/A']:
2066	drawAtoms.ClearSelection()
2067	else:
2068	if drawAtoms.GetColLabelValue(c) in ['Style','Label']:
2069	atomData[r][c] = drawAtoms.GetCellValue(r,c)
2070	FindBondsDraw()
2071	elif drawAtoms.GetColLabelValue(c) == 'Color':
2072	dlg = wx.ColourDialog(G2frame)
2073	if dlg.ShowModal() == wx.ID_OK:
2074	color = dlg.GetColourData().GetColour()
2075	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2076	attr.SetReadOnly(True)
2077	attr.SetBackgroundColour(color)
2078	atomData[r][c] = color
2079	drawingData['Atoms'][r][c] = color
2080	drawAtoms.SetAttr(i,cs+2,attr)
2081	dlg.Destroy()
2082	UpdateDrawAtoms()
2083	G2plt.PlotStructure(G2frame,data)
2084
2085	def RowSelect(event):
2086	r,c = event.GetRow(),event.GetCol()
2087	if r < 0 and c < 0:
2088	if drawAtoms.IsSelection():
2089	drawAtoms.ClearSelection()
2090	elif c < 0: #only row clicks
2091	if event.ControlDown():
2092	if r in drawAtoms.GetSelectedRows():
2093	drawAtoms.DeselectRow(r)
2094	else:
2095	drawAtoms.SelectRow(r,True)
2096	elif event.ShiftDown():
2097	indxs = drawAtoms.GetSelectedRows()
2098	drawAtoms.ClearSelection()
2099	ibeg = 0
2100	if indxs:
2101	ibeg = indxs[-1]
2102	for row in range(ibeg,r+1):
2103	drawAtoms.SelectRow(row,True)
2104	else:
2105	drawAtoms.ClearSelection()
2106	drawAtoms.SelectRow(r,True)
2107	drawingData['selectedAtoms'] = []
2108	drawingData['selectedAtoms'] = drawAtoms.GetSelectedRows()
2109	G2plt.PlotStructure(G2frame,data)
2110
2111	# UpdateDrawAtoms executable code starts here
2112	G2frame.dataFrame.SetStatusText('')
2113	generalData = data['General']
2114	SetupDrawingData()
2115	drawingData = data['Drawing']
2116	cx,ct,cs,ci = drawingData['atomPtrs']
2117	atomData = drawingData['Atoms']
2118	if atomStyle:
2119	for atom in atomData:
2120	atom[cs] = atomStyle
2121	Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',]+ \
2122	[wg.GRID_VALUE_STRING,wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,polyhedra",
2123	wg.GRID_VALUE_CHOICE+": ,type,name,number",wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,]
2124	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2125	labelChoice = [' ','type','name','number']
2126	colLabels = ['Name','Type','x','y','z','Sym Op','Style','Label','Color','I/A']
2127	if generalData['Type'] == 'macromolecular':
2128	colLabels = ['Residue','1-letter','Chain'] + colLabels
2129	Types = 3*[wg.GRID_VALUE_STRING,]+Types
2130	Types[8] = wg.GRID_VALUE_CHOICE+": ,lines,vdW balls,sticks,balls & sticks,ellipsoids,backbone,ribbons,schematic"
2131	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','backbone','ribbons','schematic']
2132	labelChoice = [' ','type','name','number','residue','1-letter','chain']
2133	Types[9] = wg.GRID_VALUE_CHOICE+": ,type,name,number,residue,1-letter,chain"
2134	# elif generalData['Type'] == 'modulated':
2135	# Types += []
2136	# colLabels += []
2137	table = []
2138	rowLabels = []
2139	for i,atom in enumerate(drawingData['Atoms']):
2140	table.append(atom[:colLabels.index('I/A')+1])
2141	rowLabels.append(str(i))
2142
2143	atomTable = G2gd.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
2144	drawAtoms.SetTable(atomTable, True)
2145	drawAtoms.SetMargins(0,0)
2146	drawAtoms.AutoSizeColumns(True)
2147	drawAtoms.SetColSize(colLabels.index('Style'),80)
2148	drawAtoms.SetColSize(colLabels.index('Color'),50)
2149	drawAtoms.Bind(wg.EVT_GRID_CELL_CHANGE, RefreshAtomGrid)
2150	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, RefreshAtomGrid)
2151	drawAtoms.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, RefreshAtomGrid)
2152	drawAtoms.Bind(wg.EVT_GRID_LABEL_LEFT_CLICK, RowSelect)
2153	for i,atom in enumerate(drawingData['Atoms']):
2154	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2155	attr.SetReadOnly(True)
2156	attr.SetBackgroundColour(atom[cs+2])
2157	drawAtoms.SetAttr(i,cs+2,attr)
2158	drawAtoms.SetCellValue(i,cs+2,'')
2159	indx = drawingData['selectedAtoms']
2160	if indx:
2161	for r in range(len(atomData)):
2162	if r in indx:
2163	drawAtoms.SelectRow(r)
2164	for c in range(len(colLabels)):
2165	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2166	attr.SetReadOnly(True)
2167	attr.SetBackgroundColour(VERY_LIGHT_GREY)
2168	if colLabels[c] not in ['Style','Label','Color']:
2169	drawAtoms.SetColAttr(c,attr)
2170	G2frame.dataFrame.setSizePosLeft([600,300])
2171
2172	FindBondsDraw()
2173	drawAtoms.ClearSelection()
2174	# G2plt.PlotStructure(G2frame,data)
2175
2176	def DrawAtomStyle(event):
2177	indx = drawAtoms.GetSelectedRows()
2178	if indx:
2179	generalData = data['General']
2180	atomData = data['Drawing']['Atoms']
2181	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2182	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids','polyhedra']
2183	if generalData['Type'] == 'macromolecular':
2184	styleChoice = [' ','lines','vdW balls','sticks','balls & sticks','ellipsoids',
2185	'backbone','ribbons','schematic']
2186	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom drawing style',styleChoice)
2187	if dlg.ShowModal() == wx.ID_OK:
2188	sel = dlg.GetSelection()
2189	parms = styleChoice[sel]
2190	for r in indx:
2191	atomData[r][cs] = parms
2192	drawAtoms.SetCellValue(r,cs,parms)
2193	dlg.Destroy()
2194	FindBondsDraw()
2195	drawAtoms.ClearSelection()
2196	G2plt.PlotStructure(G2frame,data)
2197
2198	def DrawAtomLabel(event):
2199	indx = drawAtoms.GetSelectedRows()
2200	if indx:
2201	generalData = data['General']
2202	atomData = data['Drawing']['Atoms']
2203	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2204	styleChoice = [' ','type','name','number']
2205	if generalData['Type'] == 'macromolecular':
2206	styleChoice = [' ','type','name','number','residue','1-letter','chain']
2207	dlg = wx.SingleChoiceDialog(G2frame,'Select','Atom label style',styleChoice)
2208	if dlg.ShowModal() == wx.ID_OK:
2209	sel = dlg.GetSelection()
2210	parms = styleChoice[sel]
2211	for r in indx:
2212	atomData[r][cs+1] = parms
2213	drawAtoms.SetCellValue(r,cs+1,parms)
2214	dlg.Destroy()
2215	drawAtoms.ClearSelection()
2216	G2plt.PlotStructure(G2frame,data)
2217
2218	def DrawAtomColor(event):
2219
2220	indx = drawAtoms.GetSelectedRows()
2221	if indx:
2222	if len(indx) > 1:
2223	G2frame.dataFrame.SetStatusText('Select Custom Color, change color, Add to Custom Colors, then OK')
2224	else:
2225	G2frame.dataFrame.SetStatusText('Change color, Add to Custom Colors, then OK')
2226	generalData = data['General']
2227	atomData = data['Drawing']['Atoms']
2228	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2229	atmColors = []
2230	atmTypes = []
2231	for r in indx:
2232	if atomData[r][cs+2] not in atmColors:
2233	atmColors.append(atomData[r][cs+2])
2234	atmTypes.append(atomData[r][ct])
2235	if len(atmColors) > 16:
2236	break
2237	colors = wx.ColourData()
2238	colors.SetChooseFull(True)
2239	dlg = wx.ColourDialog(G2frame)
2240	if dlg.ShowModal() == wx.ID_OK:
2241	for i in range(len(atmColors)):
2242	atmColors[i] = dlg.GetColourData().GetColour()
2243	colorDict = dict(zip(atmTypes,atmColors))
2244	for r in indx:
2245	color = colorDict[atomData[r][ct]]
2246	atomData[r][cs+2] = color
2247	attr = wg.GridCellAttr() #needs to be here - gets lost if outside loop!
2248	attr.SetBackgroundColour(color)
2249	drawAtoms.SetAttr(r,cs+2,attr)
2250	data['Drawing']['Atoms'][r][cs+2] = color
2251	drawAtoms.ClearSelection()
2252	dlg.Destroy()
2253	G2frame.dataFrame.SetStatusText('')
2254	G2plt.PlotStructure(G2frame,data)
2255
2256	def ResetAtomColors(event):
2257	generalData = data['General']
2258	atomData = data['Drawing']['Atoms']
2259	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2260	for atom in atomData:
2261	atNum = generalData['AtomTypes'].index(atom[ct])
2262	atom[cs+2] = list(generalData['Color'][atNum])
2263	UpdateDrawAtoms()
2264	drawAtoms.ClearSelection()
2265	G2plt.PlotStructure(G2frame,data)
2266
2267	def SetViewPoint(event):
2268	indx = drawAtoms.GetSelectedRows()
2269	if indx:
2270	atomData = data['Drawing']['Atoms']
2271	cx = data['Drawing']['atomPtrs'][0]
2272	data['Drawing']['viewPoint'] = [atomData[indx[0]][cx:cx+3],[indx[0],0]]
2273	drawAtoms.ClearSelection() #do I really want to do this?
2274	G2plt.PlotStructure(G2frame,data)
2275
2276	def noDuplicate(xyz,atomData): #be careful where this is used - it's slow
2277	cx = data['Drawing']['atomPtrs'][0]
2278	if True in [np.allclose(np.array(xyz),np.array(atom[cx:cx+3]),atol=0.0002) for atom in atomData]:
2279	return False
2280	else:
2281	return True
2282
2283	def AddSymEquiv(event):
2284	indx = drawAtoms.GetSelectedRows()
2285	indx.sort()
2286	if indx:
2287	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2288	cx = colLabels.index('x')
2289	cuia = colLabels.index('I/A')
2290	cuij = cuia+2
2291	atomData = data['Drawing']['Atoms']
2292	generalData = data['General']
2293	SGData = generalData['SGData']
2294	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2295	try:
2296	if dlg.ShowModal() == wx.ID_OK:
2297	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2298	Cell = np.array(Cell)
2299	cent = SGData['SGCen'][Cent]
2300	M,T = SGData['SGOps'][Opr]
2301	for ind in indx:
2302	XYZ = np.array(atomData[ind][cx:cx+3])
2303	XYZ = np.inner(M,XYZ)+T
2304	if Inv:
2305	XYZ = -XYZ
2306	XYZ = XYZ+cent+Cell
2307	if Force:
2308	XYZ = G2spc.MoveToUnitCell(XYZ)
2309	if noDuplicate(XYZ,atomData):
2310	atom = copy.copy(atomData[ind])
2311	atom[cx:cx+3] = XYZ
2312	atomOp = atom[cx+3]
2313	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2314	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2315	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2316	if atom[cuia] == 'A':
2317	Uij = atom[cuij:cuij+6]
2318	U = G2spc.Uij2U(Uij)
2319	U = np.inner(np.inner(M,U),M)
2320	Uij = G2spc.U2Uij(U)
2321	atom[cuij:cuij+6] = Uij
2322	atomData.append(atom)
2323	finally:
2324	dlg.Destroy()
2325	UpdateDrawAtoms()
2326	drawAtoms.ClearSelection()
2327	G2plt.PlotStructure(G2frame,data)
2328
2329	def TransformSymEquiv(event):
2330	indx = drawAtoms.GetSelectedRows()
2331	indx.sort()
2332	if indx:
2333	atomData = data['Drawing']['Atoms']
2334	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2335	cx = colLabels.index('x')
2336	cuia = colLabels.index('I/A')
2337	cuij = cuia+2
2338	atomData = data['Drawing']['Atoms']
2339	generalData = data['General']
2340	SGData = generalData['SGData']
2341	dlg = G2gd.SymOpDialog(G2frame,SGData,False,True)
2342	try:
2343	if dlg.ShowModal() == wx.ID_OK:
2344	Inv,Cent,Opr,Cell,New,Force = dlg.GetSelection()
2345	Cell = np.array(Cell)
2346	cent = SGData['SGCen'][Cent]
2347	M,T = SGData['SGOps'][Opr]
2348	for ind in indx:
2349	XYZ = np.array(atomData[ind][cx:cx+3])
2350	XYZ = np.inner(M,XYZ)+T
2351	if Inv:
2352	XYZ = -XYZ
2353	XYZ = XYZ+cent+Cell
2354	if Force:
2355	XYZ = G2spc.MoveToUnitCell(XYZ)
2356	atom = atomData[ind]
2357	atom[cx:cx+3] = XYZ
2358	atomOp = atom[cx+3]
2359	newOp = str(((Opr+1)+100Cent)(1-2*Inv))+'+'+ \
2360	str(int(Cell[0]))+','+str(int(Cell[1]))+','+str(int(Cell[2]))
2361	atom[cx+3] = G2spc.StringOpsProd(atomOp,newOp,SGData)
2362	if atom[cuia] == 'A':
2363	Uij = atom[cuij:cuij+6]
2364	U = G2spc.Uij2U(Uij)
2365	U = np.inner(np.inner(M,U),M)
2366	Uij = G2spc.U2Uij(U)
2367	atom[cuij:cuij+6] = Uij
2368	data['Drawing']['Atoms'] = atomData
2369	finally:
2370	dlg.Destroy()
2371	UpdateDrawAtoms()
2372	drawAtoms.ClearSelection()
2373	G2plt.PlotStructure(G2frame,data)
2374
2375	def FillCoordSphere(event):
2376	generalData = data['General']
2377	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2378	radii = generalData['BondRadii']
2379	atomTypes = generalData['AtomTypes']
2380	try:
2381	indH = atomTypes.index('H')
2382	radii[indH] = 0.5
2383	except:
2384	pass
2385	indx = drawAtoms.GetSelectedRows()
2386	if indx:
2387	indx.sort()
2388	atomData = data['Drawing']['Atoms']
2389	numAtoms = len(atomData)
2390	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2391	generalData = data['General']
2392	SGData = generalData['SGData']
2393	cellArray = G2lat.CellBlock(1)
2394	wx.BeginBusyCursor()
2395	try:
2396	for ind in indx:
2397	atomA = atomData[ind]
2398	xyzA = np.array(atomA[cx:cx+3])
2399	indA = atomTypes.index(atomA[ct])
2400	for atomB in atomData[:numAtoms]:
2401	indB = atomTypes.index(atomB[ct])
2402	sumR = radii[indA]+radii[indB]
2403	xyzB = np.array(atomB[cx:cx+3])
2404	for xyz in cellArray+xyzB:
2405	dist = np.sqrt(np.sum(np.inner(Amat,xyz-xyzA)**2))
2406	if 0 < dist <= data['Drawing']['radiusFactor']*sumR:
2407	if noDuplicate(xyz,atomData):
2408	oprB = atomB[cx+3]
2409	C = xyz-xyzB
2410	newOp = '1+'+str(int(round(C[0])))+','+str(int(round(C[1])))+','+str(int(round(C[2])))
2411	newAtom = atomB[:]
2412	newAtom[cx:cx+3] = xyz
2413	newAtom[cx+3] = G2spc.StringOpsProd(oprB,newOp,SGData)
2414	atomData.append(newAtom)
2415	finally:
2416	wx.EndBusyCursor()
2417	data['Drawing']['Atoms'] = atomData
2418	UpdateDrawAtoms()
2419	drawAtoms.ClearSelection()
2420	G2plt.PlotStructure(G2frame,data)
2421
2422	def FillUnitCell(event):
2423	indx = drawAtoms.GetSelectedRows()
2424	indx.sort()
2425	if indx:
2426	atomData = data['Drawing']['Atoms']
2427	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2428	cx = colLabels.index('x')
2429	cuia = colLabels.index('I/A')
2430	cuij = cuia+2
2431	generalData = data['General']
2432	SGData = generalData['SGData']
2433	wx.BeginBusyCursor()
2434	try:
2435	for ind in indx:
2436	atom = atomData[ind]
2437	XYZ = np.array(atom[cx:cx+3])
2438	if atom[cuia] == 'A':
2439	Uij = atom[cuij:cuij+6]
2440	result = G2spc.GenAtom(XYZ,SGData,False,Uij,False)
2441	for item in result:
2442	atom = copy.copy(atomData[ind])
2443	atom[cx:cx+3] = item[0]
2444	atom[cx+3] = str(item[2])+'+' \
2445	+str(item[3][0])+','+str(item[3][1])+','+str(item[3][2])
2446	atom[cuij:cuij+6] = item[1]
2447	Opp = G2spc.Opposite(item[0])
2448	for xyz in Opp:
2449	if noDuplicate(xyz,atomData):
2450	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2451	cell = '1'+'+'+ \
2452	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2453	atom[cx:cx+3] = xyz
2454	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2455	atomData.append(atom[:])
2456	else:
2457	result = G2spc.GenAtom(XYZ,SGData,False,Move=False)
2458	for item in result:
2459	atom = copy.copy(atomData[ind])
2460	atom[cx:cx+3] = item[0]
2461	atom[cx+3] = str(item[1])+'+' \
2462	+str(item[2][0])+','+str(item[2][1])+','+str(item[2][2])
2463	Opp = G2spc.Opposite(item[0])
2464	for xyz in Opp:
2465	if noDuplicate(xyz,atomData):
2466	cell = np.asarray(np.rint(xyz-atom[cx:cx+3]),dtype=np.int32)
2467	cell = '1'+'+'+ \
2468	str(cell[0])+','+str(cell[1])+','+str(cell[2])
2469	atom[cx:cx+3] = xyz
2470	atom[cx+3] = G2spc.StringOpsProd(cell,atom[cx+3],SGData)
2471	atomData.append(atom[:])
2472	data['Drawing']['Atoms'] = atomData
2473	finally:
2474	wx.EndBusyCursor()
2475	UpdateDrawAtoms()
2476	drawAtoms.ClearSelection()
2477	G2plt.PlotStructure(G2frame,data)
2478
2479	def FindBondsToo(): #works but slow for large structures - keep as reference
2480	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2481	atomData = data['Drawing']['Atoms']
2482	generalData = data['General']
2483	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2484	radii = generalData['BondRadii']
2485	atomTypes = generalData['AtomTypes']
2486	try:
2487	indH = atomTypes.index('H')
2488	radii[indH] = 0.5
2489	except:
2490	pass
2491	for atom in atomData:
2492	atom[-1] = []
2493	Atoms = []
2494	for i,atom in enumerate(atomData):
2495	Atoms.append([i,np.array(atom[cx:cx+3]),atom[cs],radii[atomTypes.index(atom[ct])]])
2496	for atomA in Atoms:
2497	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2498	for atomB in Atoms:
2499	Dx = atomB[1]-atomA[1]
2500	DX = np.inner(Amat,Dx)
2501	dist = np.sqrt(np.sum(DX**2))
2502	sumR = atomA[3]+atomB[3]
2503	if 0.5 < dist <= 0.85*sumR:
2504	i = atomA[0]
2505	if atomA[2] == 'polyhedra':
2506	atomData[i][-1].append(DX)
2507	elif atomB[1] != 'polyhedra':
2508	j = atomB[0]
2509	atomData[i][-1].append(Dx*atomA[3]/sumR)
2510	atomData[j][-1].append(-Dx*atomB[3]/sumR)
2511
2512	def FindBondsDraw(): #uses numpy & masks - very fast even for proteins!
2513	import numpy.ma as ma
2514	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2515	hydro = data['Drawing']['showHydrogen']
2516	atomData = data['Drawing']['Atoms']
2517	generalData = data['General']
2518	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2519	radii = generalData['BondRadii']
2520	atomTypes = generalData['AtomTypes']
2521	try:
2522	indH = atomTypes.index('H')
2523	radii[indH] = 0.5
2524	except:
2525	pass
2526	for atom in atomData:
2527	atom[-2] = [] #clear out old bonds/polyhedra
2528	atom[-1] = []
2529	Indx = range(len(atomData))
2530	Atoms = []
2531	Styles = []
2532	Radii = []
2533	for atom in atomData:
2534	Atoms.append(np.array(atom[cx:cx+3]))
2535	Styles.append(atom[cs])
2536	try:
2537	if not hydro and atom[ct] == 'H':
2538	Radii.append(0.0)
2539	else:
2540	Radii.append(radii[atomTypes.index(atom[ct])])
2541	except ValueError: #changed atom type!
2542	Radii.append(0.20)
2543	Atoms = np.array(Atoms)
2544	Radii = np.array(Radii)
2545	IASR = zip(Indx,Atoms,Styles,Radii)
2546	for atomA in IASR:
2547	if atomA[2] in ['lines','sticks','ellipsoids','balls & sticks','polyhedra']:
2548	Dx = Atoms-atomA[1]
2549	dist = ma.masked_less(np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0)),0.5) #gets rid of G2frame & disorder "bonds" < 0.5A
2550	sumR = atomA[3]+Radii
2551	IndB = ma.nonzero(ma.masked_greater(dist-data['Drawing']['radiusFactor']*sumR,0.)) #get indices of bonded atoms
2552	i = atomA[0]
2553	for j in IndB[0]:
2554	if Styles[i] == 'polyhedra':
2555	atomData[i][-2].append(np.inner(Amat,Dx[j]))
2556	elif Styles[j] != 'polyhedra' and j > i:
2557	atomData[i][-2].append(Dx[j]*Radii[i]/sumR[j])
2558	atomData[j][-2].append(-Dx[j]*Radii[j]/sumR[j])
2559	if Styles[i] == 'polyhedra':
2560	Bonds = atomData[i][-2]
2561	Faces = []
2562	if len(Bonds) > 2:
2563	FaceGen = G2lat.uniqueCombinations(Bonds,3) #N.B. this is a generator
2564	for face in FaceGen:
2565	vol = nl.det(face)
2566	if abs(vol) > 1. or len(Bonds) == 3:
2567	if vol < 0.:
2568	face = [face[0],face[2],face[1]]
2569	face = np.array(face)
2570	if not np.array([np.array(nl.det(face-bond))+0.0001 < 0 for bond in Bonds]).any():
2571	norm = np.cross(face[1]-face[0],face[2]-face[0])
2572	norm /= np.sqrt(np.sum(norm**2))
2573	Faces.append([face,norm])
2574	atomData[i][-1] = Faces
2575
2576	def DrawAtomsDelete(event):
2577	indx = drawAtoms.GetSelectedRows()
2578	indx.sort()
2579	if indx:
2580	atomData = data['Drawing']['Atoms']
2581	indx.reverse()
2582	for ind in indx:
2583	del atomData[ind]
2584	UpdateDrawAtoms()
2585	drawAtoms.ClearSelection()
2586	G2plt.PlotStructure(G2frame,data)
2587	event.StopPropagation()
2588
2589	def OnReloadDrawAtoms(event):
2590	data['Drawing']['Atoms'] = []
2591	UpdateDrawAtoms()
2592	drawAtoms.ClearSelection()
2593	G2plt.PlotStructure(G2frame,data)
2594	event.StopPropagation()
2595
2596	def DrawAtomsDeleteByIDs(IDs):
2597	atomData = data['Drawing']['Atoms']
2598	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2599	indx.reverse()
2600	for ind in indx:
2601	del atomData[ind]
2602
2603	def ChangeDrawAtomsByIDs(colName,IDs,value):
2604	atomData = data['Drawing']['Atoms']
2605	cx,ct,cs,ci = data['Drawing']['atomPtrs']
2606	if colName == 'Name':
2607	col = ct-1
2608	elif colName == 'Type':
2609	col = ct
2610	elif colName == 'I/A':
2611	col = cs
2612	indx = G2mth.FindAtomIndexByIDs(atomData,IDs)
2613	for ind in indx:
2614	atomData[ind][col] = value
2615
2616	def OnDrawPlane(event):
2617	indx = drawAtoms.GetSelectedRows()
2618	if len(indx) < 4:
2619	print '**** ERROR - need 4+ atoms for plane calculation'
2620	return
2621	PlaneData = {}
2622	drawingData = data['Drawing']
2623	atomData = drawingData['Atoms']
2624	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2625	cx = colLabels.index('x')
2626	cn = colLabels.index('Name')
2627	xyz = []
2628	for i,atom in enumerate(atomData):
2629	if i in indx:
2630	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
2631	generalData = data['General']
2632	PlaneData['Name'] = generalData['Name']
2633	PlaneData['Atoms'] = xyz
2634	PlaneData['Cell'] = generalData['Cell'][1:] #+ volume
2635	G2stMn.BestPlane(PlaneData)
2636
2637	def OnDrawDistVP(event):
2638	# distance to view point
2639	indx = drawAtoms.GetSelectedRows()
2640	if not indx:
2641	print '***** ERROR - no atoms selected'
2642	return
2643	generalData = data['General']
2644	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2645	drawingData = data['Drawing']
2646	viewPt = np.array(drawingData['viewPoint'][0])
2647	print ' Distance from view point at %.3f %.3f %.3f to:'%(viewPt[0],viewPt[1],viewPt[2])
2648	atomDData = drawingData['Atoms']
2649	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2650	cx = colLabels.index('x')
2651	cn = colLabels.index('Name')
2652	for i in indx:
2653	atom = atomDData[i]
2654	Dx = np.array(atom[cx:cx+3])-viewPt
2655	dist = np.sqrt(np.sum(np.inner(Amat,Dx)**2,axis=0))
2656	print 'Atom: %8s (%12s) distance = %.3f'%(atom[cn],atom[cx+3],dist)
2657
2658	def OnDrawDAT(event):
2659	#distance, angle, torsion
2660	indx = drawAtoms.GetSelectedRows()
2661	if len(indx) not in [2,3,4]:
2662	print '**** ERROR - wrong number of atoms for distance, angle or torsion calculation'
2663	return
2664	DATData = {}
2665	ocx,oct,ocs,cia = data['General']['AtomPtrs']
2666	drawingData = data['Drawing']
2667	atomData = data['Atoms']
2668	atomDData = drawingData['Atoms']
2669	colLabels = [drawAtoms.GetColLabelValue(c) for c in range(drawAtoms.GetNumberCols())]
2670	cx = colLabels.index('x')
2671	cn = colLabels.index('Name')
2672	cid = colLabels.index('I/A')+8
2673	xyz = []
2674	Oxyz = []
2675	DATData['Natoms'] = len(indx)
2676	for i in indx:
2677	atom = atomDData[i]
2678	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+4]) #also gets Sym Op
2679	id = G2mth.FindAtomIndexByIDs(atomData,[atom[cid],],False)[0]
2680	Oxyz.append([id,]+atomData[id][cx+1:cx+4])
2681	DATData['Datoms'] = xyz
2682	DATData['Oatoms'] = Oxyz
2683	generalData = data['General']
2684	DATData['Name'] = generalData['Name']
2685	DATData['SGData'] = generalData['SGData']
2686	DATData['Cell'] = generalData['Cell'][1:] #+ volume
2687	if 'pId' in data:
2688	DATData['pId'] = data['pId']
2689	DATData['covData'] = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Covariance'))
2690	G2stMn.DisAglTor(DATData)
2691
2692	################################################################################
2693	#### Draw Options page
2694	################################################################################
2695
2696	def UpdateDrawOptions():
2697	import copy
2698	import wx.lib.colourselect as wcs
2699	def SlopSizer():
2700	def OnCameraPos(event):
2701	drawingData['cameraPos'] = cameraPos.GetValue()
2702	cameraPosTxt.SetLabel(' Camera Distance: '+'%.2f'%(drawingData['cameraPos']))
2703	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2704	G2plt.PlotStructure(G2frame,data)
2705
2706	def OnZclip(event):
2707	drawingData['Zclip'] = Zclip.GetValue()
2708	ZclipTxt.SetLabel(' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2709	G2plt.PlotStructure(G2frame,data)
2710
2711	def OnZstep(event):
2712	try:
2713	step = float(Zstep.GetValue())
2714	if not (0.01 <= step <= 1.0):
2715	raise ValueError
2716	except ValueError:
2717	step = drawingData['Zstep']
2718	drawingData['Zstep'] = step
2719	Zstep.SetValue('%.2fA'%(drawingData['Zstep']))
2720
2721	def OnMoveZ(event):
2722	move = MoveZ.GetValue()*drawingData['Zstep']
2723	MoveZ.SetValue(0)
2724	VP = np.inner(Amat,np.array(drawingData['viewPoint'][0]))
2725	VD = np.inner(Amat,np.array(drawingData['viewDir']))
2726	VD /= np.sqrt(np.sum(VD**2))
2727	VP += move*VD
2728	VP = np.inner(Bmat,VP)
2729	drawingData['viewPoint'][0] = VP
2730	panel = drawOptions.GetChildren()
2731	names = [child.GetName() for child in panel]
2732	panel[names.index('viewPoint')].SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2733	G2plt.PlotStructure(G2frame,data)
2734
2735	def OnVdWScale(event):
2736	drawingData['vdwScale'] = vdwScale.GetValue()/100.
2737	vdwScaleTxt.SetLabel(' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2738	G2plt.PlotStructure(G2frame,data)
2739
2740	def OnEllipseProb(event):
2741	drawingData['ellipseProb'] = ellipseProb.GetValue()
2742	ellipseProbTxt.SetLabel(' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2743	G2plt.PlotStructure(G2frame,data)
2744
2745	def OnBallScale(event):
2746	drawingData['ballScale'] = ballScale.GetValue()/100.
2747	ballScaleTxt.SetLabel(' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2748	G2plt.PlotStructure(G2frame,data)
2749
2750	def OnBondRadius(event):
2751	drawingData['bondRadius'] = bondRadius.GetValue()/100.
2752	bondRadiusTxt.SetLabel(' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2753	G2plt.PlotStructure(G2frame,data)
2754
2755	def OnContourLevel(event):
2756	drawingData['contourLevel'] = contourLevel.GetValue()/100.
2757	contourLevelTxt.SetLabel(' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2758	G2plt.PlotStructure(G2frame,data)
2759
2760	def OnMapSize(event):
2761	drawingData['mapSize'] = mapSize.GetValue()/10.
2762	mapSizeTxt.SetLabel(' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2763	G2plt.PlotStructure(G2frame,data)
2764
2765
2766	slopSizer = wx.BoxSizer(wx.HORIZONTAL)
2767	slideSizer = wx.FlexGridSizer(0,2)
2768	slideSizer.AddGrowableCol(1,1)
2769
2770	cameraPosTxt = wx.StaticText(drawOptions,-1,
2771	' Camera Distance: '+'%.2f'%(drawingData['cameraPos']),name='cameraPos')
2772	G2frame.dataDisplay.cameraPosTxt = cameraPosTxt
2773	slideSizer.Add(cameraPosTxt,0,WACV)
2774	cameraPos = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['cameraPos'],name='cameraSlider')
2775	cameraPos.SetRange(10,500)
2776	cameraPos.Bind(wx.EVT_SLIDER, OnCameraPos)
2777	G2frame.dataDisplay.cameraSlider = cameraPos
2778	slideSizer.Add(cameraPos,1,wx.EXPAND\|wx.RIGHT)
2779
2780	ZclipTxt = wx.StaticText(drawOptions,-1,' Z clipping: '+'%.2fA'%(drawingData['Zclip']*drawingData['cameraPos']/100.))
2781	slideSizer.Add(ZclipTxt,0,WACV)
2782	Zclip = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['Zclip'])
2783	Zclip.SetRange(1,99)
2784	Zclip.Bind(wx.EVT_SLIDER, OnZclip)
2785	slideSizer.Add(Zclip,1,wx.EXPAND\|wx.RIGHT)
2786
2787	ZstepSizer = wx.BoxSizer(wx.HORIZONTAL)
2788	ZstepSizer.Add(wx.StaticText(drawOptions,-1,' Z step:'),0,WACV)
2789	Zstep = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['Zstep']),
2790	style=wx.TE_PROCESS_ENTER)
2791	Zstep.Bind(wx.EVT_TEXT_ENTER,OnZstep)
2792	Zstep.Bind(wx.EVT_KILL_FOCUS,OnZstep)
2793	ZstepSizer.Add(Zstep,0,WACV)
2794	slideSizer.Add(ZstepSizer)
2795	MoveSizer = wx.BoxSizer(wx.HORIZONTAL)
2796	MoveSizer.Add(wx.StaticText(drawOptions,-1,' Press to step:'),0,WACV)
2797	MoveZ = wx.SpinButton(drawOptions,style=wx.SP_HORIZONTAL,size=wx.Size(100,20))
2798	MoveZ.SetValue(0)
2799	MoveZ.SetRange(-1,1)
2800	MoveZ.Bind(wx.EVT_SPIN, OnMoveZ)
2801	MoveSizer.Add(MoveZ)
2802	slideSizer.Add(MoveSizer,1,wx.EXPAND\|wx.RIGHT)
2803
2804	vdwScaleTxt = wx.StaticText(drawOptions,-1,' van der Waals scale: '+'%.2f'%(drawingData['vdwScale']))
2805	slideSizer.Add(vdwScaleTxt,0,WACV)
2806	vdwScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['vdwScale']))
2807	vdwScale.Bind(wx.EVT_SLIDER, OnVdWScale)
2808	slideSizer.Add(vdwScale,1,wx.EXPAND\|wx.RIGHT)
2809
2810	ellipseProbTxt = wx.StaticText(drawOptions,-1,' Ellipsoid probability: '+'%d%%'%(drawingData['ellipseProb']))
2811	slideSizer.Add(ellipseProbTxt,0,WACV)
2812	ellipseProb = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=drawingData['ellipseProb'])
2813	ellipseProb.SetRange(1,99)
2814	ellipseProb.Bind(wx.EVT_SLIDER, OnEllipseProb)
2815	slideSizer.Add(ellipseProb,1,wx.EXPAND\|wx.RIGHT)
2816
2817	ballScaleTxt = wx.StaticText(drawOptions,-1,' Ball scale: '+'%.2f'%(drawingData['ballScale']))
2818	slideSizer.Add(ballScaleTxt,0,WACV)
2819	ballScale = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['ballScale']))
2820	ballScale.Bind(wx.EVT_SLIDER, OnBallScale)
2821	slideSizer.Add(ballScale,1,wx.EXPAND\|wx.RIGHT)
2822
2823	bondRadiusTxt = wx.StaticText(drawOptions,-1,' Bond radius, A: '+'%.2f'%(drawingData['bondRadius']))
2824	slideSizer.Add(bondRadiusTxt,0,WACV)
2825	bondRadius = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['bondRadius']))
2826	bondRadius.SetRange(1,25)
2827	bondRadius.Bind(wx.EVT_SLIDER, OnBondRadius)
2828	slideSizer.Add(bondRadius,1,wx.EXPAND\|wx.RIGHT)
2829
2830	if generalData['Map']['rhoMax']:
2831	contourLevelTxt = wx.StaticText(drawOptions,-1,' Contour level: '+'%.2f'%(drawingData['contourLevel']*generalData['Map']['rhoMax']))
2832	slideSizer.Add(contourLevelTxt,0,WACV)
2833	contourLevel = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(100*drawingData['contourLevel']))
2834	contourLevel.SetRange(1,100)
2835	contourLevel.Bind(wx.EVT_SLIDER, OnContourLevel)
2836	slideSizer.Add(contourLevel,1,wx.EXPAND\|wx.RIGHT)
2837	mapSizeTxt = wx.StaticText(drawOptions,-1,' Map radius, A: '+'%.1f'%(drawingData['mapSize']))
2838	slideSizer.Add(mapSizeTxt,0,WACV)
2839	mapSize = wx.Slider(drawOptions,style=wx.SL_HORIZONTAL,value=int(10*drawingData['mapSize']))
2840	mapSize.SetRange(1,100)
2841	mapSize.Bind(wx.EVT_SLIDER, OnMapSize)
2842	slideSizer.Add(mapSize,1,wx.EXPAND\|wx.RIGHT)
2843
2844	slopSizer.Add(slideSizer,1,wx.EXPAND\|wx.RIGHT)
2845	slopSizer.Add((10,5),0)
2846	slopSizer.SetMinSize(wx.Size(350,10))
2847	return slopSizer
2848
2849	def ShowSizer():
2850
2851	def OnBackColor(event):
2852	drawingData['backColor'] = event.GetValue()
2853	G2plt.PlotStructure(G2frame,data)
2854
2855	def OnShowABC(event):
2856	drawingData['showABC'] = showABC.GetValue()
2857	G2plt.PlotStructure(G2frame,data)
2858
2859	def OnShowUnitCell(event):
2860	drawingData['unitCellBox'] = unitCellBox.GetValue()
2861	G2plt.PlotStructure(G2frame,data)
2862
2863	def OnShowHyd(event):
2864	drawingData['showHydrogen'] = showHydrogen.GetValue()
2865	FindBondsDraw()
2866	G2plt.PlotStructure(G2frame,data)
2867
2868	def OnShowRB(event):
2869	drawingData['showRigidBodies'] = showRB.GetValue()
2870	FindBondsDraw()
2871	G2plt.PlotStructure(G2frame,data)
2872
2873	def OnViewPoint(event):
2874	Obj = event.GetEventObject()
2875	viewPt = Obj.GetValue().split()
2876	try:
2877	VP = [float(viewPt[i]) for i in range(3)]
2878	except (ValueError,IndexError):
2879	VP = drawingData['viewPoint'][0]
2880	Obj.SetValue('%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]))
2881	drawingData['viewPoint'][0] = VP
2882	G2plt.PlotStructure(G2frame,data)
2883
2884	def OnViewDir(event):
2885	Obj = event.GetEventObject()
2886	viewDir = Obj.GetValue().split()
2887	try:
2888	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2889	VD = np.array([float(viewDir[i]) for i in range(3)])
2890	VC = np.inner(Amat,VD)
2891	VC /= np.sqrt(np.sum(VC**2))
2892	V = np.array(drawingData['viewDir'])
2893	VB = np.inner(Amat,V)
2894	VB /= np.sqrt(np.sum(VB**2))
2895	VX = np.cross(VC,VB)
2896	A = acosd(max((2.-np.sum((VB-VC)**2))/2.,-1.))
2897	QV = G2mth.AVdeg2Q(A,VX)
2898	Q = drawingData['Quaternion']
2899	drawingData['Quaternion'] = G2mth.prodQQ(Q,QV)
2900	except (ValueError,IndexError):
2901	VD = drawingData['viewDir']
2902	Obj.SetValue('%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]))
2903	drawingData['viewDir'] = VD
2904	G2plt.PlotStructure(G2frame,data)
2905
2906	showSizer = wx.BoxSizer(wx.VERTICAL)
2907	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2908	lineSizer.Add(wx.StaticText(drawOptions,-1,' Background color:'),0,WACV)
2909	backColor = wcs.ColourSelect(drawOptions, -1,colour=drawingData['backColor'],size=wx.Size(25,25))
2910	backColor.Bind(wcs.EVT_COLOURSELECT, OnBackColor)
2911	lineSizer.Add(backColor,0,WACV)
2912	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Dir.:'),0,WACV)
2913	VD = drawingData['viewDir']
2914	viewDir = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VD[0],VD[1],VD[2]),
2915	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewDir')
2916	viewDir.Bind(wx.EVT_TEXT_ENTER,OnViewDir)
2917	viewDir.Bind(wx.EVT_KILL_FOCUS,OnViewDir)
2918	G2frame.dataDisplay.viewDir = viewDir
2919	lineSizer.Add(viewDir,0,WACV)
2920	showSizer.Add(lineSizer)
2921	showSizer.Add((0,5),0)
2922
2923	lineSizer = wx.BoxSizer(wx.HORIZONTAL)
2924	showABC = wx.CheckBox(drawOptions,-1,label=' Show view point?')
2925	showABC.Bind(wx.EVT_CHECKBOX, OnShowABC)
2926	showABC.SetValue(drawingData['showABC'])
2927	lineSizer.Add(showABC,0,WACV)
2928	lineSizer.Add(wx.StaticText(drawOptions,-1,' View Point:'),0,WACV)
2929	VP = drawingData['viewPoint'][0]
2930	viewPoint = wx.TextCtrl(drawOptions,value='%.3f %.3f %.3f'%(VP[0],VP[1],VP[2]),
2931	style=wx.TE_PROCESS_ENTER,size=wx.Size(140,20),name='viewPoint')
2932	G2frame.dataDisplay.viewPoint = viewPoint
2933	viewPoint.Bind(wx.EVT_TEXT_ENTER,OnViewPoint)
2934	viewPoint.Bind(wx.EVT_KILL_FOCUS,OnViewPoint)
2935	lineSizer.Add(viewPoint,0,WACV)
2936	showSizer.Add(lineSizer)
2937	showSizer.Add((0,5),0)
2938
2939	line2Sizer = wx.BoxSizer(wx.HORIZONTAL)
2940
2941	unitCellBox = wx.CheckBox(drawOptions,-1,label=' Show unit cell?')
2942	unitCellBox.Bind(wx.EVT_CHECKBOX, OnShowUnitCell)
2943	unitCellBox.SetValue(drawingData['unitCellBox'])
2944	line2Sizer.Add(unitCellBox,0,WACV)
2945
2946	showHydrogen = wx.CheckBox(drawOptions,-1,label=' Show hydrogens?')
2947	showHydrogen.Bind(wx.EVT_CHECKBOX, OnShowHyd)
2948	showHydrogen.SetValue(drawingData['showHydrogen'])
2949	line2Sizer.Add(showHydrogen,0,WACV)
2950
2951	showRB = wx.CheckBox(drawOptions,-1,label=' Show rigid Bodies?')
2952	showRB.Bind(wx.EVT_CHECKBOX, OnShowRB)
2953	showRB.SetValue(drawingData['showRigidBodies'])
2954	line2Sizer.Add(showRB,0,WACV)
2955
2956	showSizer.Add(line2Sizer)
2957	return showSizer
2958
2959	def RadSizer():
2960
2961	def OnSizeHatoms(event):
2962	try:
2963	value = max(0.1,min(1.2,float(sizeH.GetValue())))
2964	except ValueError:
2965	value = 0.5
2966	drawingData['sizeH'] = value
2967	sizeH.SetValue("%.2f"%(value))
2968	G2plt.PlotStructure(G2frame,data)
2969
2970	def OnRadFactor(event):
2971	try:
2972	value = max(0.1,min(1.2,float(radFactor.GetValue())))
2973	except ValueError:
2974	value = 0.85
2975	drawingData['radiusFactor'] = value
2976	radFactor.SetValue("%.2f"%(value))
2977	FindBondsDraw()
2978	G2plt.PlotStructure(G2frame,data)
2979
2980	radSizer = wx.BoxSizer(wx.HORIZONTAL)
2981	radSizer.Add(wx.StaticText(drawOptions,-1,' Hydrogen radius, A: '),0,WACV)
2982	sizeH = wx.TextCtrl(drawOptions,-1,value='%.2f'%(drawingData['sizeH']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2983	sizeH.Bind(wx.EVT_TEXT_ENTER,OnSizeHatoms)
2984	sizeH.Bind(wx.EVT_KILL_FOCUS,OnSizeHatoms)
2985	radSizer.Add(sizeH,0,WACV)
2986
2987	radSizer.Add(wx.StaticText(drawOptions,-1,' Bond search factor: '),0,WACV)
2988	radFactor = wx.TextCtrl(drawOptions,value='%.2f'%(drawingData['radiusFactor']),size=wx.Size(60,20),style=wx.TE_PROCESS_ENTER)
2989	radFactor.Bind(wx.EVT_TEXT_ENTER,OnRadFactor)
2990	radFactor.Bind(wx.EVT_KILL_FOCUS,OnRadFactor)
2991	radSizer.Add(radFactor,0,WACV)
2992	return radSizer
2993
2994	# UpdateDrawOptions exectable code starts here
2995	generalData = data['General']
2996	Amat,Bmat = G2lat.cell2AB(generalData['Cell'][1:7])
2997	SetupDrawingData()
2998	drawingData = data['Drawing']
2999	if generalData['Type'] == 'nuclear':
3000	pickChoice = ['Atoms','Bonds','Torsions','Planes']
3001	elif generalData['Type'] == 'macromolecular':
3002	pickChoice = ['Atoms','Residues','Chains','Bonds','Torsions','Planes','phi/psi']
3003
3004	G2frame.dataFrame.SetStatusText('')
3005	if drawOptions.GetSizer():
3006	drawOptions.GetSizer().Clear(True)
3007	mainSizer = wx.BoxSizer(wx.VERTICAL)
3008	mainSizer.Add((5,5),0)
3009	mainSizer.Add(wx.StaticText(drawOptions,-1,' Drawing controls:'),0,WACV)
3010	mainSizer.Add((5,5),0)
3011	mainSizer.Add(SlopSizer(),0)
3012	mainSizer.Add((5,5),0)
3013	mainSizer.Add(ShowSizer(),0,)
3014	mainSizer.Add((5,5),0)
3015	mainSizer.Add(RadSizer(),0,)
3016	SetPhaseWindow(G2frame.dataFrame,drawOptions,mainSizer)
3017
3018	################################################################################
3019	#### Texture routines
3020	################################################################################
3021
3022	def UpdateTexture():
3023	def SetSHCoef():
3024	cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],SamSym[textureData['Model']],textureData['Order'])
3025	newSHCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
3026	SHCoeff = textureData['SH Coeff'][1]
3027	for cofName in SHCoeff:
3028	if cofName in cofNames:
3029	newSHCoef[cofName] = SHCoeff[cofName]
3030	return newSHCoef
3031
3032	def OnShOrder(event):
3033	Obj = event.GetEventObject()
3034	textureData['Order'] = int(Obj.GetValue())
3035	textureData['SH Coeff'][1] = SetSHCoef()
3036	wx.CallAfter(UpdateTexture)
3037	G2plt.PlotTexture(G2frame,data)
3038
3039	def OnShModel(event):
3040	Obj = event.GetEventObject()
3041	textureData['Model'] = Obj.GetValue()
3042	textureData['SH Coeff'][1] = SetSHCoef()
3043	wx.CallAfter(UpdateTexture)
3044	G2plt.PlotTexture(G2frame,data)
3045
3046	def OnSHRefine(event):
3047	Obj = event.GetEventObject()
3048	textureData['SH Coeff'][0] = Obj.GetValue()
3049
3050	def OnSHShow(event):
3051	Obj = event.GetEventObject()
3052	textureData['SHShow'] = Obj.GetValue()
3053	wx.CallAfter(UpdateTexture)
3054
3055	def OnProjSel(event):
3056	Obj = event.GetEventObject()
3057	G2frame.Projection = Obj.GetValue()
3058	G2plt.PlotTexture(G2frame,data)
3059
3060	def OnColorSel(event):
3061	Obj = event.GetEventObject()
3062	G2frame.ContourColor = Obj.GetValue()
3063	G2plt.PlotTexture(G2frame,data)
3064
3065	def OnAngRef(event):
3066	Obj = event.GetEventObject()
3067	textureData[angIndx[Obj.GetId()]][0] = Obj.GetValue()
3068
3069	def OnAngValue(event):
3070	Obj = event.GetEventObject()
3071	try:
3072	value = float(Obj.GetValue())
3073	except ValueError:
3074	value = textureData[valIndx[Obj.GetId()]][1]
3075	Obj.SetValue('%8.2f'%(value))
3076	textureData[valIndx[Obj.GetId()]][1] = value
3077
3078	def OnODFValue(event):
3079	Obj = event.GetEventObject()
3080	try:
3081	value = float(Obj.GetValue())
3082	except ValueError:
3083	value = textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]]
3084	Obj.SetValue('%8.3f'%(value))
3085	textureData['SH Coeff'][1][ODFIndx[Obj.GetId()]] = value
3086	G2plt.PlotTexture(G2frame,data)
3087
3088	def OnPfType(event):
3089	Obj = event.GetEventObject()
3090	textureData['PlotType'] = Obj.GetValue()
3091	wx.CallAfter(UpdateTexture)
3092	G2plt.PlotTexture(G2frame,data)
3093
3094	def OnPFValue(event):
3095	Obj = event.GetEventObject()
3096	Saxis = Obj.GetValue().split()
3097	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3098	try:
3099	hkl = [int(Saxis[i]) for i in range(3)]
3100	except (ValueError,IndexError):
3101	hkl = textureData['PFhkl']
3102	if not np.any(np.array(hkl)): #can't be all zeros!
3103	hkl = textureData['PFhkl']
3104	Obj.SetValue('%d %d %d'%(hkl[0],hkl[1],hkl[2]))
3105	textureData['PFhkl'] = hkl
3106	else:
3107	try:
3108	xyz = [float(Saxis[i]) for i in range(3)]
3109	except (ValueError,IndexError):
3110	xyz = textureData['PFxyz']
3111	if not np.any(np.array(xyz)): #can't be all zeros!
3112	xyz = textureData['PFxyz']
3113	Obj.SetValue('%3.1f %3.1f %3.1f'%(xyz[0],xyz[1],xyz[2]))
3114	textureData['PFxyz'] = xyz
3115	G2plt.PlotTexture(G2frame,data)
3116
3117	# UpdateTexture executable starts here
3118	G2frame.dataFrame.SetStatusText('')
3119	generalData = data['General']
3120	SGData = generalData['SGData']
3121	try:
3122	textureData = generalData['SH Texture']
3123	except KeyError: #fix old files!
3124	textureData = generalData['SH Texture'] = {'Order':0,'Model':'cylindrical',
3125	'Sample omega':[False,0.0],'Sample chi':[False,0.0],'Sample phi':[False,0.0],
3126	'SH Coeff':[False,{}],'SHShow':False,'PFhkl':[0,0,1],
3127	'PFxyz':[0,0,1.],'PlotType':'Pole figure'}
3128	if 'SHShow' not in textureData: #another fix
3129	textureData.update({'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3130	try: #another fix!
3131	x = textureData['PlotType']
3132	except KeyError:
3133	textureData.update({'PFxyz':[0,0,1.],'PlotType':'Pole figure'})
3134	shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
3135	SamSym = dict(zip(shModels,['0','-1','2/m','mmm']))
3136	shAngles = ['omega','chi','phi']
3137	if Texture.GetSizer():
3138	Texture.GetSizer().Clear(True)
3139	mainSizer = wx.BoxSizer(wx.VERTICAL)
3140	titleSizer = wx.BoxSizer(wx.HORIZONTAL)
3141	titleSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonics texture data for '+PhaseName+':'),0,WACV)
3142	titleSizer.Add(wx.StaticText(Texture,-1,
3143	' Texture Index J = %7.3f'%(G2lat.textureIndex(textureData['SH Coeff'][1]))),
3144	0,WACV)
3145	mainSizer.Add(titleSizer,0)
3146	mainSizer.Add((0,5),0)
3147	shSizer = wx.FlexGridSizer(0,6,5,5)
3148	shSizer.Add(wx.StaticText(Texture,-1,'Texture model: '),0,WACV)
3149	shModel = wx.ComboBox(Texture,-1,value=textureData['Model'],choices=shModels,
3150	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3151	shModel.Bind(wx.EVT_COMBOBOX,OnShModel)
3152	shSizer.Add(shModel,0,WACV)
3153	shSizer.Add(wx.StaticText(Texture,-1,' Harmonic order: '),0,WACV)
3154	shOrder = wx.ComboBox(Texture,-1,value=str(textureData['Order']),choices=[str(2*i) for i in range(18)],
3155	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3156	shOrder.Bind(wx.EVT_COMBOBOX,OnShOrder)
3157	shSizer.Add(shOrder,0,WACV)
3158	shRef = wx.CheckBox(Texture,-1,label=' Refine texture?')
3159	shRef.SetValue(textureData['SH Coeff'][0])
3160	shRef.Bind(wx.EVT_CHECKBOX, OnSHRefine)
3161	shSizer.Add(shRef,0,WACV)
3162	shShow = wx.CheckBox(Texture,-1,label=' Show coeff.?')
3163	shShow.SetValue(textureData['SHShow'])
3164	shShow.Bind(wx.EVT_CHECKBOX, OnSHShow)
3165	shSizer.Add(shShow,0,WACV)
3166	mainSizer.Add(shSizer,0,0)
3167	mainSizer.Add((0,5),0)
3168	PTSizer = wx.FlexGridSizer(0,4,5,5)
3169	PTSizer.Add(wx.StaticText(Texture,-1,' Texture plot type: '),0,WACV)
3170	choices = ['Axial pole distribution','Pole figure','Inverse pole figure']
3171	pfType = wx.ComboBox(Texture,-1,value=str(textureData['PlotType']),choices=choices,
3172	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3173	pfType.Bind(wx.EVT_COMBOBOX,OnPfType)
3174	PTSizer.Add(pfType,0,WACV)
3175	if 'Axial' not in textureData['PlotType']:
3176	PTSizer.Add(wx.StaticText(Texture,-1,' Projection type: '),0,WACV)
3177	projSel = wx.ComboBox(Texture,-1,value=G2frame.Projection,choices=['equal area','stereographic','3D display'],
3178	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3179	projSel.Bind(wx.EVT_COMBOBOX,OnProjSel)
3180	PTSizer.Add(projSel,0,WACV)
3181	if textureData['PlotType'] in ['Pole figure','Axial pole distribution']:
3182	PTSizer.Add(wx.StaticText(Texture,-1,' Pole figure HKL: '),0,WACV)
3183	PH = textureData['PFhkl']
3184	pfVal = wx.TextCtrl(Texture,-1,'%d %d %d'%(PH[0],PH[1],PH[2]),style=wx.TE_PROCESS_ENTER)
3185	else:
3186	PTSizer.Add(wx.StaticText(Texture,-1,' Inverse pole figure XYZ: '),0,WACV)
3187	PX = textureData['PFxyz']
3188	pfVal = wx.TextCtrl(Texture,-1,'%3.1f %3.1f %3.1f'%(PX[0],PX[1],PX[2]),style=wx.TE_PROCESS_ENTER)
3189	pfVal.Bind(wx.EVT_TEXT_ENTER,OnPFValue)
3190	pfVal.Bind(wx.EVT_KILL_FOCUS,OnPFValue)
3191	PTSizer.Add(pfVal,0,WACV)
3192	if 'Axial' not in textureData['PlotType']:
3193	PTSizer.Add(wx.StaticText(Texture,-1,' Color scheme'),0,WACV)
3194	choice = [m for m in mpl.cm.datad.keys() if not m.endswith("_r")]
3195	choice.sort()
3196	colorSel = wx.ComboBox(Texture,-1,value=G2frame.ContourColor,choices=choice,
3197	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3198	colorSel.Bind(wx.EVT_COMBOBOX,OnColorSel)
3199	PTSizer.Add(colorSel,0,WACV)
3200	mainSizer.Add(PTSizer,0,WACV)
3201	mainSizer.Add((0,5),0)
3202	if textureData['SHShow']:
3203	mainSizer.Add(wx.StaticText(Texture,-1,'Spherical harmonic coefficients: '),0,WACV)
3204	mainSizer.Add((0,5),0)
3205	ODFSizer = wx.FlexGridSizer(0,8,2,2)
3206	ODFIndx = {}
3207	ODFkeys = textureData['SH Coeff'][1].keys()
3208	ODFkeys.sort()
3209	for item in ODFkeys:
3210	ODFSizer.Add(wx.StaticText(Texture,-1,item),0,WACV)
3211	ODFval = wx.TextCtrl(Texture,wx.ID_ANY,'%8.3f'%(textureData['SH Coeff'][1][item]),style=wx.TE_PROCESS_ENTER)
3212	ODFIndx[ODFval.GetId()] = item
3213	ODFval.Bind(wx.EVT_TEXT_ENTER,OnODFValue)
3214	ODFval.Bind(wx.EVT_KILL_FOCUS,OnODFValue)
3215	ODFSizer.Add(ODFval,0,WACV)
3216	mainSizer.Add(ODFSizer,0,WACV)
3217	mainSizer.Add((0,5),0)
3218	mainSizer.Add((0,5),0)
3219	mainSizer.Add(wx.StaticText(Texture,-1,'Sample orientation angles: '),0,WACV)
3220	mainSizer.Add((0,5),0)
3221	angSizer = wx.BoxSizer(wx.HORIZONTAL)
3222	angIndx = {}
3223	valIndx = {}
3224	for item in ['Sample omega','Sample chi','Sample phi']:
3225	angRef = wx.CheckBox(Texture,-1,label=item+': ')
3226	angRef.SetValue(textureData[item][0])
3227	angIndx[angRef.GetId()] = item
3228	angRef.Bind(wx.EVT_CHECKBOX, OnAngRef)
3229	angSizer.Add(angRef,0,WACV)
3230	angVal = wx.TextCtrl(Texture,wx.ID_ANY,'%8.2f'%(textureData[item][1]),style=wx.TE_PROCESS_ENTER)
3231	valIndx[angVal.GetId()] = item
3232	angVal.Bind(wx.EVT_TEXT_ENTER,OnAngValue)
3233	angVal.Bind(wx.EVT_KILL_FOCUS,OnAngValue)
3234	angSizer.Add(angVal,0,WACV)
3235	angSizer.Add((5,0),0)
3236	mainSizer.Add(angSizer,0,WACV)
3237	SetPhaseWindow(G2frame.dataFrame,Texture,mainSizer)
3238
3239	################################################################################
3240	##### DData routines - GUI stuff in GSASIIddataGUI.py
3241	################################################################################
3242
3243	def OnHklfAdd(event):
3244	UseList = data['Histograms']
3245	keyList = UseList.keys()
3246	TextList = []
3247	if not G2frame.PatternTree.GetCount():
3248	return
3249
3250	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3251	while item:
3252	name = G2frame.PatternTree.GetItemText(item)
3253	if name not in keyList and 'HKLF' in name:
3254	TextList.append(name)
3255	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3256	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3257	try:
3258	if dlg.ShowModal() == wx.ID_OK:
3259	result = dlg.GetSelections()
3260	else:
3261	return
3262	finally:
3263	dlg.Destroy()
3264
3265	# get the histograms used in other phases
3266	phaseRIdList,usedHistograms = G2frame.GetPhaseInfofromTree()
3267	usedHKLFhists = [] # used single-crystal histograms
3268	for p in usedHistograms:
3269	for h in usedHistograms[p]:
3270	if h.startswith('HKLF ') and h not in usedHKLFhists:
3271	usedHKLFhists.append(h)
3272	# check that selected single crystal histograms are not already in use!
3273	for i in result:
3274	used = [TextList[i] for i in result if TextList[i] in usedHKLFhists]
3275	if used:
3276	msg = 'The following single crystal histogram(s) are already in use'
3277	for i in used:
3278	msg += '\n '+str(i)
3279	msg += '\nAre you sure you want to add them to this phase? '
3280	msg += 'Associating a single crystal dataset to >1 histogram is usually an error, '
3281	msg += 'so No is suggested here.'
3282	if G2frame.ErrorDialog('Likely error',msg,G2frame,wtype=wx.YES_NO) != wx.ID_YES: return
3283
3284	wx.BeginBusyCursor()
3285	for i in result:
3286	histoName = TextList[i]
3287	UseList[histoName] = {'Histogram':histoName,'Show':False,'Scale':[1.0,True],
3288	'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]},
3289	'Extinction':['Lorentzian','None',
3290	{'Tbar':0.1,'Cos2TM':0.955,'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]},]}
3291	UpdateHKLFdata(histoName)
3292	data['Histograms'] = UseList
3293	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3294	wx.EndBusyCursor()
3295
3296	def UpdateHKLFdata(histoName):
3297	generalData = data['General']
3298	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3299	refDict,reflData = G2frame.PatternTree.GetItemPyData(Id)
3300	SGData = generalData['SGData']
3301	Cell = generalData['Cell'][1:7]
3302	G,g = G2lat.cell2Gmat(Cell)
3303	for iref,ref in enumerate(reflData['RefList']):
3304	H = list(ref[:3])
3305	ref[4] = np.sqrt(1./G2lat.calc_rDsq2(H,G))
3306	iabsnt,ref[3],Uniq,phi = G2spc.GenHKLf(H,SGData)
3307	#G2frame.PatternTree.SetItemPyData(Id,[refDict,reflData]) #removed by BHT -- not needed!
3308
3309	def OnPwdrAdd(event):
3310	generalData = data['General']
3311	SGData = generalData['SGData']
3312	UseList = data['Histograms']
3313	newList = []
3314	NShkl = len(G2spc.MustrainNames(SGData))
3315	NDij = len(G2spc.HStrainNames(SGData))
3316	keyList = UseList.keys()
3317	TextList = ['All PWDR']
3318	if G2frame.PatternTree.GetCount():
3319	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
3320	while item:
3321	name = G2frame.PatternTree.GetItemText(item)
3322	if name not in keyList and 'PWDR' in name:
3323	TextList.append(name)
3324	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
3325	dlg = wx.MultiChoiceDialog(G2frame, 'Which new data to use?', 'Use data', TextList, wx.CHOICEDLG_STYLE)
3326	try:
3327	if dlg.ShowModal() == wx.ID_OK:
3328	result = dlg.GetSelections()
3329	for i in result: newList.append(TextList[i])
3330	if 'All PWDR' in newList:
3331	newList = TextList[1:]
3332	for histoName in newList:
3333	Id = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,histoName)
3334	UseList[histoName] = {'Histogram':histoName,'Show':False,
3335	'Scale':[1.0,False],'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{}],
3336	'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1],
3337	[1.,1.,1.,0.,0.,0.],6*[False,]],
3338	'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1],
3339	NShkl[0.01,],NShkl[False,]],
3340	'HStrain':[NDij[0.0,],NDij[False,]],
3341	'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
3342	refList = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Reflection Lists'))
3343	refList[generalData['Name']] = []
3344	data['Histograms'] = UseList
3345	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3346	finally:
3347	dlg.Destroy()
3348
3349	def OnDataDelete(event):
3350	UseList = data['Histograms']
3351	keyList = ['All',]+UseList.keys()
3352	keyList.sort()
3353	DelList = []
3354	if UseList:
3355	DelList = []
3356	dlg = wx.MultiChoiceDialog(G2frame,
3357	'Which histogram to delete from this phase?', 'Delete histogram',
3358	keyList, wx.CHOICEDLG_STYLE)
3359	try:
3360	if dlg.ShowModal() == wx.ID_OK:
3361	result = dlg.GetSelections()
3362	for i in result:
3363	DelList.append(keyList[i])
3364	if 'All' in DelList:
3365	DelList = keyList[1:]
3366	for i in DelList:
3367	del UseList[i]
3368	wx.CallAfter(G2ddG.UpdateDData,G2frame,DData,data)
3369	finally:
3370	dlg.Destroy()
3371
3372	################################################################################
3373	##### Rigid bodies
3374	################################################################################
3375
3376	def FillRigidBodyGrid(refresh=True):
3377	'''Fill the Rigid Body Phase information tab page.
3378	Note that the page is a ScrolledWindow, not a Grid
3379	'''
3380	def OnThermSel(event): #needs to be seen by VecRbSizer!
3381	Obj = event.GetEventObject()
3382	RBObj = Indx[Obj.GetId()]
3383	val = Obj.GetValue()
3384	Ttype = 'A'
3385	if val == 'Uiso':
3386	Ttype = 'I'
3387	RBObj['ThermalMotion'][0] = 'Uiso'
3388	elif val == 'T':
3389	RBObj['ThermalMotion'][0] = 'T'
3390	elif val == 'TL':
3391	RBObj['ThermalMotion'][0] = 'TL'
3392	elif val == 'TLS':
3393	RBObj['ThermalMotion'][0] = 'TLS'
3394	wx.CallAfter(FillRigidBodyGrid,True)
3395	if val != 'None':
3396	cia = data['General']['AtomPtrs'][3]
3397	for i,id in enumerate(RBObj['Ids']):
3398	data['Atoms'][AtLookUp[id]][cia] = Ttype
3399	G2plt.PlotStructure(G2frame,data)
3400
3401	def ThermDataSizer(RBObj,rbType):
3402
3403	def OnThermval(event):
3404	Obj = event.GetEventObject()
3405	item = Indx[Obj.GetId()]
3406	try:
3407	val = float(Obj.GetValue())
3408	RBObj['ThermalMotion'][1][item] = val
3409	except ValueError:
3410	pass
3411	Obj.SetValue('%8.4f'%(RBObj['ThermalMotion'][1][item]))
3412	Cart = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[1]
3413	Uout = G2mth.UpdateRBUIJ(Bmat,Cart,RBObj)
3414	cia = data['General']['AtomPtrs'][3]
3415	for i,id in enumerate(RBObj['Ids']):
3416	if Uout[i][0] == 'I':
3417	data['Atoms'][AtLookUp[id]][cia+1] = Uout[i][1]
3418	else:
3419	data['Atoms'][AtLookUp[id]][cia+2:cia+8] = Uout[i][2:8]
3420	G2plt.PlotStructure(G2frame,data)
3421
3422	def OnTLSRef(event):
3423	Obj = event.GetEventObject()
3424	item = Indx[Obj.GetId()]
3425	RBObj['ThermalMotion'][2][item] = Obj.GetValue()
3426
3427	thermSizer = wx.FlexGridSizer(0,9,5,5)
3428	model = RBObj['ThermalMotion']
3429	if model[0] == 'Uiso':
3430	names = ['Uiso',]
3431	elif 'T' in model[0]:
3432	names = ['T11','T22','T33','T12','T13','T23']
3433	if 'L' in model[0]:
3434	names += ['L11','L22','L33','L12','L13','L23']
3435	if 'S' in model[0]:
3436	names += ['S12','S13','S21','S23','S31','S32','SAA','SBB']
3437	for i,name in enumerate(names):
3438	thermSizer.Add(wx.StaticText(RigidBodies,-1,name+': '),0,WACV)
3439	thermVal = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(model[1][i]),
3440	style=wx.TE_PROCESS_ENTER)
3441	thermVal.Bind(wx.EVT_TEXT_ENTER,OnThermval)
3442	thermVal.Bind(wx.EVT_KILL_FOCUS,OnThermval)
3443	Indx[thermVal.GetId()] = i
3444	thermSizer.Add(thermVal)
3445	Tcheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3446	Tcheck.Bind(wx.EVT_CHECKBOX,OnTLSRef)
3447	Tcheck.SetValue(model[2][i])
3448	Indx[Tcheck.GetId()] = i
3449	thermSizer.Add(Tcheck,0,WACV)
3450	return thermSizer
3451
3452	def LocationSizer(RBObj,rbType):
3453
3454	def OnOrigRef(event):
3455	RBObj['Orig'][1] = Ocheck.GetValue()
3456
3457	def OnOrienRef(event):
3458	RBObj['Orient'][1] = Qcheck.GetValue()
3459
3460	def OnOrigX(event):
3461	Obj = event.GetEventObject()
3462	item = Indx[Obj.GetId()]
3463	try:
3464	val = float(Obj.GetValue())
3465	RBObj['Orig'][0][item] = val
3466	Obj.SetValue('%8.5f'%(val))
3467	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3468	for i,id in enumerate(RBObj['Ids']):
3469	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3470	data['Drawing']['Atoms'] = []
3471	UpdateDrawAtoms(atomStyle)
3472	G2plt.PlotStructure(G2frame,data)
3473	except ValueError:
3474	pass
3475
3476	def OnOrien(event):
3477	Obj = event.GetEventObject()
3478	item = Indx[Obj.GetId()]
3479	A,V = G2mth.Q2AVdeg(RBObj['Orient'][0])
3480	V = np.inner(Bmat,V)
3481	try:
3482	val = float(Obj.GetValue())
3483	if item:
3484	V[item-1] = val
3485	else:
3486	A = val
3487	Obj.SetValue('%8.5f'%(val))
3488	V = np.inner(Amat,V)
3489	Q = G2mth.AVdeg2Q(A,V)
3490	if not any(Q):
3491	raise ValueError
3492	RBObj['Orient'][0] = Q
3493	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,rbType)[0]
3494	for i,id in enumerate(RBObj['Ids']):
3495	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3496	data['Drawing']['Atoms'] = []
3497	UpdateDrawAtoms(atomStyle)
3498	G2plt.PlotStructure(G2frame,data)
3499	except ValueError:
3500	pass
3501
3502	topSizer = wx.FlexGridSizer(0,6,5,5)
3503	Orig = RBObj['Orig'][0]
3504	Orien,OrienV = G2mth.Q2AVdeg(RBObj['Orient'][0])
3505	Orien = [Orien,]
3506	Orien.extend(OrienV/nl.norm(OrienV))
3507	topSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z:'),0,WACV)
3508	for ix,x in enumerate(Orig):
3509	origX = wx.TextCtrl(RigidBodies,-1,value='%8.5f'%(x),style=wx.TE_PROCESS_ENTER)
3510	origX.Bind(wx.EVT_TEXT_ENTER,OnOrigX)
3511	origX.Bind(wx.EVT_KILL_FOCUS,OnOrigX)
3512	Indx[origX.GetId()] = ix
3513	topSizer.Add(origX,0,WACV)
3514	topSizer.Add((5,0),)
3515	Ocheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3516	Ocheck.Bind(wx.EVT_CHECKBOX,OnOrigRef)
3517	Ocheck.SetValue(RBObj['Orig'][1])
3518	topSizer.Add(Ocheck,0,WACV)
3519	topSizer.Add(wx.StaticText(RigidBodies,-1,'Rotation angle, vector:'),0,WACV)
3520	for ix,x in enumerate(Orien):
3521	orien = wx.TextCtrl(RigidBodies,-1,value='%8.4f'%(x),style=wx.TE_PROCESS_ENTER)
3522	orien.Bind(wx.EVT_TEXT_ENTER,OnOrien)
3523	orien.Bind(wx.EVT_KILL_FOCUS,OnOrien)
3524	Indx[orien.GetId()] = ix
3525	topSizer.Add(orien,0,WACV)
3526	Qcheck = wx.ComboBox(RigidBodies,-1,value='',choices=[' ','A','AV'],
3527	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3528	Qcheck.Bind(wx.EVT_COMBOBOX,OnOrienRef)
3529	Qcheck.SetValue(RBObj['Orient'][1])
3530	topSizer.Add(Qcheck)
3531	return topSizer
3532
3533	def ResrbSizer(RBObj):
3534	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3535
3536	def OnTorsionRef(event):
3537	Obj = event.GetEventObject()
3538	item = Indx[Obj.GetId()]
3539	RBObj['Torsions'][item][1] = Obj.GetValue()
3540
3541	def OnTorsion(event):
3542	Obj = event.GetEventObject()
3543	item = Indx[Obj.GetId()]
3544	try:
3545	val = float(Obj.GetValue())
3546	RBObj['Torsions'][item][0] = val
3547	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
3548	for i,id in enumerate(RBObj['Ids']):
3549	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
3550	except ValueError:
3551	pass
3552	Obj.SetValue("%10.3f"%(RBObj['Torsions'][item][0]))
3553	data['Drawing']['Atoms'] = []
3554	UpdateDrawAtoms(atomStyle)
3555	drawAtoms.ClearSelection()
3556	G2plt.PlotStructure(G2frame,data)
3557
3558	def OnDelResRB(event):
3559	Obj = event.GetEventObject()
3560	RBId = Indx[Obj.GetId()]
3561	RBData['Residue'][RBId]['useCount'] -= 1
3562	RBObjs = data['RBModels']['Residue']
3563	for rbObj in RBObjs:
3564	if RBId == rbObj['RBId']:
3565	data['RBModels']['Residue'].remove(rbObj)
3566	G2plt.PlotStructure(G2frame,data)
3567	wx.CallAfter(FillRigidBodyGrid,True)
3568
3569	resrbSizer = wx.BoxSizer(wx.VERTICAL)
3570	resrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3571	topLine = wx.BoxSizer(wx.HORIZONTAL)
3572	topLine.Add(wx.StaticText(RigidBodies,-1,
3573	'Name: '+RBObj['RBname']+RBObj['numChain']+' '),0,WACV)
3574	rbId = RBObj['RBId']
3575	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3576	delRB.Bind(wx.EVT_CHECKBOX,OnDelResRB)
3577	Indx[delRB.GetId()] = rbId
3578	topLine.Add(delRB,0,WACV)
3579	resrbSizer.Add(topLine)
3580	resrbSizer.Add(LocationSizer(RBObj,'Residue'))
3581	resrbSizer.Add(wx.StaticText(RigidBodies,-1,'Torsions:'),0,WACV)
3582	torSizer = wx.FlexGridSizer(0,6,5,5)
3583	for itors,tors in enumerate(RBObj['Torsions']):
3584	torSizer.Add(wx.StaticText(RigidBodies,-1,'Torsion '+'%d'%(itors)),0,WACV)
3585	torsTxt = wx.TextCtrl(RigidBodies,-1,value='%.3f'%(tors[0]),style=wx.TE_PROCESS_ENTER)
3586	torsTxt.Bind(wx.EVT_TEXT_ENTER,OnTorsion)
3587	torsTxt.Bind(wx.EVT_KILL_FOCUS,OnTorsion)
3588	Indx[torsTxt.GetId()] = itors
3589	torSizer.Add(torsTxt)
3590	torCheck = wx.CheckBox(RigidBodies,-1,'Refine?')
3591	torCheck.Bind(wx.EVT_CHECKBOX,OnTorsionRef)
3592	torCheck.SetValue(tors[1])
3593	Indx[torCheck.GetId()] = itors
3594	torSizer.Add(torCheck,0,WACV)
3595	resrbSizer.Add(torSizer)
3596	tchoice = ['None','Uiso','T','TL','TLS']
3597	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3598	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3599	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3600	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3601	Indx[thermSel.GetId()] = RBObj
3602	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3603	thermSizer.Add(thermSel,0,WACV)
3604	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3605	resrbSizer.Add(thermSizer)
3606	if RBObj['ThermalMotion'][0] != 'None':
3607	resrbSizer.Add(ThermDataSizer(RBObj,'Residue'))
3608	return resrbSizer
3609
3610	def VecrbSizer(RBObj):
3611	G2frame.dataFrame.SetStatusText('NB: Rotation vector is in crystallographic space')
3612
3613	def OnDelVecRB(event):
3614	Obj = event.GetEventObject()
3615	RBId = Indx[Obj.GetId()]
3616	RBData['Vector'][RBId]['useCount'] -= 1
3617	RBObjs = data['RBModels']['Vector']
3618	for rbObj in RBObjs:
3619	if RBId == rbObj['RBId']:
3620	data['RBModels']['Vector'].remove(rbObj)
3621	G2plt.PlotStructure(G2frame,data)
3622	wx.CallAfter(FillRigidBodyGrid,True)
3623
3624	vecrbSizer = wx.BoxSizer(wx.VERTICAL)
3625	vecrbSizer.Add(wx.StaticText(RigidBodies,-1,120*'-'))
3626	topLine = wx.BoxSizer(wx.HORIZONTAL)
3627	topLine.Add(wx.StaticText(RigidBodies,-1,
3628	'Name: '+RBObj['RBname']+' '),0,WACV)
3629	rbId = RBObj['RBId']
3630	delRB = wx.CheckBox(RigidBodies,-1,'Delete?')
3631	delRB.Bind(wx.EVT_CHECKBOX,OnDelVecRB)
3632	Indx[delRB.GetId()] = rbId
3633	topLine.Add(delRB,0,WACV)
3634	vecrbSizer.Add(topLine)
3635	vecrbSizer.Add(LocationSizer(RBObj,'Vector'))
3636	tchoice = ['None','Uiso','T','TL','TLS']
3637	thermSizer = wx.BoxSizer(wx.HORIZONTAL)
3638	thermSizer.Add(wx.StaticText(RigidBodies,-1,'Rigid body thermal motion model: '),0,WACV)
3639	thermSel = wx.ComboBox(RigidBodies,-1,value=RBObj['ThermalMotion'][0],choices=tchoice,
3640	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3641	Indx[thermSel.GetId()] = RBObj
3642	thermSel.Bind(wx.EVT_COMBOBOX,OnThermSel)
3643	thermSizer.Add(thermSel,0,WACV)
3644	thermSizer.Add(wx.StaticText(RigidBodies,-1,' Units: T A^2, L deg^2, S deg-A'),0,WACV)
3645	vecrbSizer.Add(thermSizer)
3646	if RBObj['ThermalMotion'][0] != 'None':
3647	vecrbSizer.Add(ThermDataSizer(RBObj,'Vector'))
3648	return vecrbSizer
3649
3650	# FillRigidBodyGrid executable code starts here
3651	if refresh:
3652	RigidBodies.DestroyChildren()
3653	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
3654	general = data['General']
3655	cx = general['AtomPtrs'][0]
3656	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3657	RBData = G2frame.PatternTree.GetItemPyData(
3658	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3659	Indx = {}
3660	atomStyle = 'balls & sticks'
3661	if 'macro' in general['Type']:
3662	atomStyle = 'sticks'
3663	G2frame.dataFrame.SetStatusText('')
3664	mainSizer = wx.BoxSizer(wx.VERTICAL)
3665	if not data['RBModels']:
3666	mainSizer.Add((5,5),0)
3667	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No rigid body models:'),0,WACV)
3668	mainSizer.Add((5,5),0)
3669	if 'Residue' in data['RBModels']:
3670	mainSizer.Add((5,5),0)
3671	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Residue rigid bodies:'),0,WACV)
3672	mainSizer.Add((5,5),0)
3673	for RBObj in data['RBModels']['Residue']:
3674	mainSizer.Add(ResrbSizer(RBObj))
3675	if 'Vector' in data['RBModels']:
3676	mainSizer.Add((5,5),0)
3677	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Vector rigid bodies:'),0,WACV)
3678	mainSizer.Add((5,5),0)
3679	for RBObj in data['RBModels']['Vector']:
3680	mainSizer.Add(VecrbSizer(RBObj))
3681
3682	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
3683
3684	def OnRBCopyParms(event):
3685	RBObjs = []
3686	for rbType in ['Vector','Residue']:
3687	RBObjs += data['RBModels'].get(rbType,[])
3688	if not len(RBObjs):
3689	print '** ERROR - no rigid bodies defined **'
3690	return
3691	if len(RBObjs) == 1:
3692	print '** INFO - only one rigid body defined; nothing to copy to **'
3693	return
3694	Source = []
3695	sourceRB = {}
3696	for RBObj in RBObjs:
3697	Source.append(RBObj['RBname'])
3698	dlg = wx.SingleChoiceDialog(G2frame,'Select source','Copy rigid body parameters',Source)
3699	if dlg.ShowModal() == wx.ID_OK:
3700	sel = dlg.GetSelection()
3701	name = Source[sel]
3702	for item in ['Orig','Orient','ThermalMotion']:
3703	sourceRB.update({item:RBObjs[sel][item],})
3704	dlg.Destroy()
3705	if not sourceRB:
3706	return
3707	dlg = wx.MultiChoiceDialog(G2frame,'Select targets','Copy rigid body parameters',Source)
3708	if dlg.ShowModal() == wx.ID_OK:
3709	sel = dlg.GetSelections()
3710	for x in sel:
3711	RBObjs[x].update(copy.copy(sourceRB))
3712	G2plt.PlotStructure(G2frame,data)
3713	wx.CallAfter(FillRigidBodyGrid(True))
3714
3715	def OnRBAssign(event):
3716
3717	G2frame.dataFrame.SetStatusText('')
3718	RBData = G2frame.PatternTree.GetItemPyData(
3719	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
3720	rbNames = {}
3721	for rbVec in RBData['Vector']:
3722	if rbVec != 'AtInfo':
3723	rbNames[RBData['Vector'][rbVec]['RBname']] =['Vector',rbVec]
3724	for rbRes in RBData['Residue']:
3725	if rbRes != 'AtInfo':
3726	rbNames[RBData['Residue'][rbRes]['RBname']] = ['Residue',rbRes]
3727	if not rbNames:
3728	print '** ERROR - no rigid bodies defined **'
3729	return
3730	general = data['General']
3731	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
3732	cx,ct = general['AtomPtrs'][:2]
3733	atomData = data['Atoms']
3734	Indx = {}
3735	atInd = [-1,-1,-1]
3736	data['testRBObj'] = {}
3737
3738	def Draw():
3739
3740	def OnOk(event):
3741	rbType = data['testRBObj']['rbType']
3742	RBObjs = data['RBModels'].get(rbType,[])
3743	rbObj = data['testRBObj']['rbObj']
3744	rbId = rbObj['RBId']
3745	newXYZ = G2mth.UpdateRBXYZ(Bmat,rbObj,RBData,rbType)[0]
3746	Ids = []
3747	dmax = 0.0
3748	oldXYZ = G2mth.getAtomXYZ(atomData,cx)
3749	for xyz in newXYZ:
3750	dist = G2mth.GetXYZDist(xyz,oldXYZ,Amat)
3751	dmax = max(dmax,np.min(dist))
3752	id = np.argmin(dist)
3753	Ids.append(atomData[id][-1])
3754	atomData[id][cx:cx+3] = xyz
3755	if dmax > 1.0:
3756	print '** WARNING - some atoms not found or misidentified **'
3757	print '** check torsion angles & try again **'
3758	OkBtn.SetLabel('Not Ready')
3759	OkBtn.Enable(False)
3760	return
3761	rbObj['Ids'] = Ids
3762	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
3763	rbObj['RBname'] += ':'+str(RBData[rbType][rbId]['useCount'])
3764	RBObjs.append(rbObj)
3765	data['RBModels'][rbType] = RBObjs
3766	RBData[rbType][rbId]['useCount'] += 1
3767	del data['testRBObj']
3768	G2plt.PlotStructure(G2frame,data)
3769	FillRigidBodyGrid(True)
3770
3771	def OnCancel(event):
3772	del data['testRBObj']
3773	FillRigidBodyGrid(True)
3774
3775	def OnRBSel(event):
3776	selection = rbSel.GetValue()
3777	rbType,rbId = rbNames[selection]
3778	data['testRBObj']['rbAtTypes'] = RBData[rbType][rbId]['rbTypes']
3779	data['testRBObj']['AtInfo'] = RBData[rbType]['AtInfo']
3780	data['testRBObj']['rbType'] = rbType
3781	data['testRBObj']['rbData'] = RBData
3782	data['testRBObj']['Sizers'] = {}
3783	rbRef = RBData[rbType][rbId]['rbRef']
3784	data['testRBObj']['rbRef'] = rbRef
3785	refType = []
3786	refName = []
3787	for ref in rbRef[:3]:
3788	reftype = data['testRBObj']['rbAtTypes'][ref]
3789	refType.append(reftype)
3790	refName.append(reftype+' '+str(rbRef[0]))
3791	atNames,AtNames = fillAtNames(refType,atomData,ct)
3792	data['testRBObj']['atNames'] = atNames
3793	data['testRBObj']['AtNames'] = AtNames
3794	data['testRBObj']['rbObj'] = {'Orig':[[0,0,0],False],
3795	'Orient':[[0.,0.,0.,1.],' '],'Ids':[],'RBId':rbId,'Torsions':[],
3796	'numChain':'','RBname':RBData[rbType][rbId]['RBname']}
3797	data['testRBObj']['torAtms'] = []
3798	for item in RBData[rbType][rbId].get('rbSeq',[]):
3799	data['testRBObj']['rbObj']['Torsions'].append([item[2],False])
3800	data['testRBObj']['torAtms'].append([-1,-1,-1])
3801	Draw()
3802
3803	def fillAtNames(refType,atomData,ct):
3804	atNames = [{},{},{}]
3805	AtNames = {}
3806	for iatm,atom in enumerate(atomData):
3807	AtNames[atom[ct-1]] = iatm
3808	for i,reftype in enumerate(refType):
3809	if atom[ct] == reftype:
3810	atNames[i][atom[ct-1]] = iatm
3811	return atNames,AtNames
3812
3813	def OnAtOrigPick(event):
3814	Obj = event.GetEventObject()
3815	item = Indx[Obj.GetId()]
3816	atName = Obj.GetValue()
3817	rbType = data['testRBObj']['rbType']
3818	atInd[0] = atNames[item][atName]
3819	if 'Vector' in rbType:
3820	rbObj = data['testRBObj']['rbObj']
3821	rbId = rbObj['RBId']
3822	rbRef = data['testRBObj']['rbRef']
3823	rbXYZ = -RBData[rbType][rbId]['rbXYZ']
3824	nref = atNames[item][atName]
3825	Oxyz = np.inner(Bmat,np.array(rbXYZ[rbRef[0]]))
3826	Nxyz = np.array(atomData[nref][cx:cx+3])
3827	Orig = Nxyz-Oxyz
3828	data['testRBObj']['rbObj']['Orig'][0] = Orig
3829	else:
3830	Orig = atomData[atNames[item][atName]][cx:cx+3]
3831	data['testRBObj']['rbObj']['Orig'][0] = Orig
3832	for x,item in zip(Orig,Xsizers):
3833	item.SetLabel('%10.5f'%(x))
3834	G2plt.PlotStructure(G2frame,data)
3835
3836	def OnAtQPick(event):
3837	Obj = event.GetEventObject()
3838	item = Indx[Obj.GetId()]
3839	atName = Obj.GetValue()
3840	atInd[item] = atNames[item][atName]
3841	if any([x<0 for x in atInd]):
3842	return
3843	OkBtn.SetLabel('OK')
3844	OkBtn.Enable(True)
3845	rbType = data['testRBObj']['rbType']
3846	rbObj = data['testRBObj']['rbObj']
3847	rbId = rbObj['RBId']
3848	rbRef = data['testRBObj']['rbRef']
3849	rbXYZ = RBData[rbType][rbId]['rbXYZ']
3850	rbOrig = rbXYZ[rbRef[0]]
3851	VAR = rbXYZ[rbRef[1]]-rbOrig
3852	VBR = rbXYZ[rbRef[2]]-rbOrig
3853	if rbType == 'Vector':
3854	Orig = np.array(atomData[atInd[0]][cx:cx+3])
3855	else:
3856	Orig = np.array(data['testRBObj']['rbObj']['Orig'][0])
3857	VAC = np.inner(Amat,np.array(atomData[atInd[1]][cx:cx+3])-Orig)
3858	VBC = np.inner(Amat,np.array(atomData[atInd[2]][cx:cx+3])-Orig)
3859	VCC = np.cross(VAR,VAC)
3860	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
3861	VAR = G2mth.prodQVQ(QuatA,VAR)
3862	VBR = G2mth.prodQVQ(QuatA,VBR)
3863	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
3864	QuatC = G2mth.prodQQ(QuatB,QuatA)
3865	data['testRBObj']['rbObj']['Orient'] = [QuatC,' ']
3866	for x,item in zip(QuatC,Osizers):
3867	item.SetLabel('%10.4f'%(x))
3868	if rbType == 'Vector':
3869	Oxyz = np.inner(Bmat,G2mth.prodQVQ(QuatC,rbOrig))
3870	Nxyz = np.array(atomData[atInd[0]][cx:cx+3])
3871	Orig = Nxyz-Oxyz
3872	data['testRBObj']['rbObj']['Orig'][0] = Orig
3873	for x,item in zip(Orig,Xsizers):
3874	item.SetLabel('%10.5f'%(x))
3875	G2plt.PlotStructure(G2frame,data)
3876
3877	def OnTorAngle(event):
3878	OkBtn.SetLabel('OK')
3879	OkBtn.Enable(True)
3880	Obj = event.GetEventObject()
3881	[tor,torSlide] = Indx[Obj.GetId()]
3882	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3883	try:
3884	value = float(Obj.GetValue())
3885	except ValueError:
3886	value = Tors[0]
3887	Tors[0] = value
3888	Obj.SetValue('%8.3f'%(value))
3889	torSlide.SetValue(int(value*10))
3890	G2plt.PlotStructure(G2frame,data)
3891
3892	def OnTorSlide(event):
3893	OkBtn.SetLabel('OK')
3894	OkBtn.Enable(True)
3895	Obj = event.GetEventObject()
3896	tor,ang = Indx[Obj.GetId()]
3897	Tors = data['testRBObj']['rbObj']['Torsions'][tor]
3898	val = float(Obj.GetValue())/10.
3899	Tors[0] = val
3900	ang.SetValue('%8.3f'%(val))
3901	G2plt.PlotStructure(G2frame,data)
3902
3903	if len(data['testRBObj']):
3904	G2plt.PlotStructure(G2frame,data)
3905
3906	RigidBodies.DestroyChildren()
3907	mainSizer = wx.BoxSizer(wx.VERTICAL)
3908	mainSizer.Add((5,5),0)
3909	if data['testRBObj']:
3910	Xsizers = []
3911	Osizers = []
3912	rbObj = data['testRBObj']['rbObj']
3913	rbName = rbObj['RBname']
3914	rbId = rbObj['RBId']
3915	Orig = rbObj['Orig'][0]
3916	Orien = rbObj['Orient'][0]
3917	rbRef = data['testRBObj']['rbRef']
3918	Torsions = rbObj['Torsions']
3919	refName = []
3920	for ref in rbRef:
3921	refName.append(data['testRBObj']['rbAtTypes'][ref]+str(ref))
3922	atNames = data['testRBObj']['atNames']
3923	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Locate rigid body : '+rbName),
3924	0,WACV)
3925	mainSizer.Add((5,5),0)
3926	OriSizer = wx.FlexGridSizer(0,5,5,5)
3927	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Origin x,y,z: '),0,WACV)
3928	for ix,x in enumerate(Orig):
3929	origX = wx.StaticText(RigidBodies,-1,'%10.5f'%(x))
3930	OriSizer.Add(origX,0,WACV)
3931	Xsizers.append(origX)
3932	OriSizer.Add((5,0),)
3933	if len(atomData):
3934	choice = atNames[0].keys()
3935	choice.sort()
3936	data['testRBObj']['Sizers']['Xsizers'] = Xsizers
3937	OriSizer.Add(wx.StaticText(RigidBodies,-1,'Orientation quaternion: '),0,WACV)
3938	for ix,x in enumerate(Orien):
3939	orien = wx.StaticText(RigidBodies,-1,'%10.4f'%(x))
3940	OriSizer.Add(orien,0,WACV)
3941	Osizers.append(orien)
3942	data['testRBObj']['Sizers']['Osizers'] = Osizers
3943	mainSizer.Add(OriSizer)
3944	mainSizer.Add((5,5),0)
3945	RefSizer = wx.FlexGridSizer(0,7,5,5)
3946	if len(atomData):
3947	RefSizer.Add(wx.StaticText(RigidBodies,-1,'Location setting: Select match to'),0,WACV)
3948	for i in [0,1,2]:
3949	choice = ['',]+atNames[i].keys()
3950	choice.sort()
3951	RefSizer.Add(wx.StaticText(RigidBodies,-1,' '+refName[i]+': '),0,WACV)
3952	atPick = wx.ComboBox(RigidBodies,-1,value='',
3953	choices=choice[1:],style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3954	if i:
3955	atPick.Bind(wx.EVT_COMBOBOX, OnAtQPick)
3956	else:
3957	atPick.Bind(wx.EVT_COMBOBOX, OnAtOrigPick)
3958	Indx[atPick.GetId()] = i
3959	RefSizer.Add(atPick,0,WACV)
3960	mainSizer.Add(RefSizer)
3961	mainSizer.Add((5,5),0)
3962	if Torsions:
3963	AtNames = data['testRBObj']['AtNames']
3964	rbAtTypes = data['testRBObj']['rbAtTypes']
3965	rbSeq = RBData['Residue'][rbId]['rbSeq']
3966	TorSizer = wx.FlexGridSizer(0,4)
3967	TorSizer.AddGrowableCol(1,1)
3968	for t,[torsion,seq] in enumerate(zip(Torsions,rbSeq)):
3969	torName = ''
3970	for item in [seq[0],seq[1],seq[3][0]]:
3971	torName += data['testRBObj']['rbAtTypes'][item]+str(item)+' '
3972	TorSizer.Add(wx.StaticText(RigidBodies,-1,'Side chain torsion for rb seq: '+torName),0,WACV)
3973	torSlide = wx.Slider(RigidBodies,style=wx.SL_HORIZONTAL)
3974	torSlide.SetRange(0,3600)
3975	torSlide.SetValue(int(torsion[0]*10.))
3976	torSlide.Bind(wx.EVT_SLIDER, OnTorSlide)
3977	TorSizer.Add(torSlide,1,wx.EXPAND\|wx.RIGHT)
3978	TorSizer.Add(wx.StaticText(RigidBodies,-1,' Angle: '),0,WACV)
3979	ang = wx.TextCtrl(RigidBodies,-1,value='%8.3f'%(torsion[0]),style=wx.TE_PROCESS_ENTER)
3980	ang.Bind(wx.EVT_TEXT_ENTER,OnTorAngle)
3981	ang.Bind(wx.EVT_KILL_FOCUS,OnTorAngle)
3982	Indx[torSlide.GetId()] = [t,ang]
3983	Indx[ang.GetId()] = [t,torSlide]
3984	TorSizer.Add(ang,0,WACV)
3985	mainSizer.Add(TorSizer,1,wx.EXPAND\|wx.RIGHT)
3986	else:
3987	mainSizer.Add(wx.StaticText(RigidBodies,-1,'No side chain torsions'),0,WACV)
3988	else:
3989	mainSizer.Add(wx.StaticText(RigidBodies,-1,'Assign rigid body:'),0,WACV)
3990	mainSizer.Add((5,5),0)
3991	topSizer = wx.BoxSizer(wx.HORIZONTAL)
3992	topSizer.Add(wx.StaticText(RigidBodies,-1,'Select rigid body model'),0,WACV)
3993	rbSel = wx.ComboBox(RigidBodies,-1,value='',choices=rbNames.keys(),
3994	style=wx.CB_READONLY\|wx.CB_DROPDOWN)
3995	rbSel.Bind(wx.EVT_COMBOBOX, OnRBSel)
3996	topSizer.Add((5,5),0)
3997	topSizer.Add(rbSel,0,WACV)
3998	mainSizer.Add(topSizer)
3999
4000	OkBtn = wx.Button(RigidBodies,-1,"Not ready")
4001	OkBtn.Bind(wx.EVT_BUTTON, OnOk)
4002	OkBtn.Enable(False)
4003	CancelBtn = wx.Button(RigidBodies,-1,'Cancel')
4004	CancelBtn.Bind(wx.EVT_BUTTON, OnCancel)
4005	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
4006	btnSizer.Add((20,20),1)
4007	btnSizer.Add(OkBtn)
4008	btnSizer.Add(CancelBtn)
4009	btnSizer.Add((20,20),1)
4010	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
4011	SetPhaseWindow(G2frame.dataFrame,RigidBodies,mainSizer)
4012	Draw()
4013
4014	def OnAutoFindResRB(event):
4015	RBData = G2frame.PatternTree.GetItemPyData(
4016	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4017	rbKeys = RBData['Residue'].keys()
4018	rbKeys.remove('AtInfo')
4019	if not len(rbKeys):
4020	print '** ERROR - no residue rigid bodies are defined **'
4021	return
4022	RBNames = [RBData['Residue'][k]['RBname'] for k in rbKeys]
4023	RBIds = dict(zip(RBNames,rbKeys))
4024	general = data['General']
4025	Amat,Bmat = G2lat.cell2AB(general['Cell'][1:7])
4026	Atoms = data['Atoms']
4027	AtLookUp = G2mth.FillAtomLookUp(Atoms)
4028	if 'macro' not in general['Type']:
4029	print '** ERROR - this phase is not a macromolecule **'
4030	return
4031	if not len(Atoms):
4032	print '** ERROR - this phase has no atoms **'
4033	return
4034	RBObjs = []
4035	cx,ct = general['AtomPtrs'][:2]
4036	iatm = 0
4037	wx.BeginBusyCursor()
4038	try:
4039	while iatm < len(Atoms):
4040	atom = Atoms[iatm]
4041	res = atom[1].strip()
4042	numChain = ' %s %s'%(atom[0],atom[2])
4043	if res not in RBIds or atom[ct-1] == 'OXT':
4044	iatm += 1
4045	continue #skip for OXT, water molecules, etc.
4046	rbRes = RBData['Residue'][RBIds[res]]
4047	rbRef = rbRes['rbRef']
4048	VAR = rbRes['rbXYZ'][rbRef[1]]-rbRes['rbXYZ'][rbRef[0]]
4049	VBR = rbRes['rbXYZ'][rbRef[2]]-rbRes['rbXYZ'][rbRef[0]]
4050	rbObj = {'RBname':rbRes['RBname']+':'+str(rbRes['useCount']),'numChain':numChain}
4051	rbAtoms = []
4052	rbIds = []
4053	for iratm in range(len(rbRes['atNames'])):
4054	rbAtoms.append(np.array(Atoms[iatm][cx:cx+3]))
4055	rbIds.append(Atoms[iatm][20])
4056	iatm += 1 #puts this at beginning of next residue?
4057	Orig = rbAtoms[rbRef[0]]
4058	rbObj['RBId'] = RBIds[res]
4059	rbObj['Ids'] = rbIds
4060	rbObj['Orig'] = [Orig,False]
4061	# print ' residue '+rbRes['RBname']+str(atom[0]).strip()+ \
4062	# ' origin at: ','%.5f %.5f %.5f'%(Orig[0],Orig[1],Orig[2])
4063	VAC = np.inner(Amat,rbAtoms[rbRef[1]]-Orig)
4064	VBC = np.inner(Amat,rbAtoms[rbRef[2]]-Orig)
4065	VCC = np.cross(VAR,VAC)
4066	QuatA = G2mth.makeQuat(VAR,VAC,VCC)[0]
4067	VAR = G2mth.prodQVQ(QuatA,VAR)
4068	VBR = G2mth.prodQVQ(QuatA,VBR)
4069	QuatB = G2mth.makeQuat(VBR,VBC,VAR)[0]
4070	QuatC = G2mth.prodQQ(QuatB,QuatA)
4071	rbObj['Orient'] = [QuatC,' ']
4072	rbObj['ThermalMotion'] = ['None',[0. for i in range(21)],[False for i in range(21)]] #type,values,flags
4073	SXYZ = []
4074	TXYZ = []
4075	rbObj['Torsions'] = []
4076	for i,xyz in enumerate(rbRes['rbXYZ']):
4077	SXYZ.append(G2mth.prodQVQ(QuatC,xyz))
4078	TXYZ.append(np.inner(Amat,rbAtoms[i]-Orig))
4079	for Oatm,Patm,x,Riders in rbRes['rbSeq']:
4080	VBR = SXYZ[Oatm]-SXYZ[Patm]
4081	VAR = SXYZ[Riders[0]]-SXYZ[Patm]
4082	VAC = TXYZ[Riders[0]]-TXYZ[Patm]
4083	QuatA,D = G2mth.makeQuat(VAR,VAC,VBR)
4084	ang = 180.*D/np.pi
4085	rbObj['Torsions'].append([ang,False])
4086	for ride in Riders:
4087	SXYZ[ride] = G2mth.prodQVQ(QuatA,SXYZ[ride]-SXYZ[Patm])+SXYZ[Patm]
4088	rbRes['useCount'] += 1
4089	RBObjs.append(rbObj)
4090	data['RBModels']['Residue'] = RBObjs
4091	for RBObj in RBObjs:
4092	newXYZ = G2mth.UpdateRBXYZ(Bmat,RBObj,RBData,'Residue')[0]
4093	for i,id in enumerate(RBObj['Ids']):
4094	data['Atoms'][AtLookUp[id]][cx:cx+3] = newXYZ[i]
4095	finally:
4096	wx.EndBusyCursor()
4097	wx.CallAfter(FillRigidBodyGrid,True)
4098
4099	def OnRBRemoveAll(event):
4100	data['RBModels']['Residue'] = []
4101	data['RBModels']['Vector'] = []
4102	RBData = G2frame.PatternTree.GetItemPyData(
4103	G2gd.GetPatternTreeItemId(G2frame,G2frame.root,'Rigid bodies'))
4104	for RBType in ['Vector','Residue']:
4105	for rbId in RBData[RBType]:
4106	RBData[RBType][rbId]['useCount'] = 0
4107	FillRigidBodyGrid(True)
4108
4109	def OnGlobalResRBTherm(event):
4110	AtLookUp = G2mth.FillAtomLookUp(data['Atoms'])
4111	RBObjs = data['RBModels']['Residue']
4112	names = ['None','Uiso','T','TL','TLS']
4113	cia = data['General']['AtomPtrs'][3]
4114	dlg = wx.SingleChoiceDialog(G2frame,'Select','Residue thermal motion model',names)
4115	if dlg.ShowModal() == wx.ID_OK:
4116	sel = dlg.GetSelection()
4117	parm = names[sel]
4118	Ttype = 'A'
4119	if parm == 'Uiso':
4120	Ttype = 'I'
4121	for rbObj in RBObjs:
4122	rbObj['ThermalMotion'][0] = parm
4123	if parm != 'None':
4124	for i,id in enumerate(rbObj['Ids']):
4125	data['Atoms'][AtLookUp[id]][cia] = Ttype
4126	dlg.Destroy()
4127	wx.CallAfter(FillRigidBodyGrid,True)
4128
4129	def OnGlobalResRBRef(event):
4130	RBObjs = data['RBModels']['Residue']
4131	names = ['Origin','Orient. angle','Full Orient.']
4132	nTor = 0
4133	for rbObj in RBObjs:
4134	nTor = max(nTor,len(rbObj['Torsions']))
4135	names += ['Torsion '+str(i) for i in range(nTor)]
4136	if np.any([rbObj['ThermalMotion'][0] == 'Uiso' for rbObj in RBObjs]):
4137	names += ['Uiso',]
4138	if np.any([rbObj['ThermalMotion'][0] == 'TLS' for rbObj in RBObjs]):
4139	names += ['Tii','Tij','Lii','Lij','Sij']
4140	elif np.any([rbObj['ThermalMotion'][0] == 'TL' for rbObj in RBObjs]):
4141	names += ['Tii','Tij','Lii','Lij']
4142	elif np.any([rbObj['ThermalMotion'][0] == 'T' for rbObj in RBObjs]):
4143	names += ['Tii','Tij']
4144
4145	dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',names)
4146	if dlg.ShowModal() == wx.ID_OK:
4147	sel = dlg.GetSelections()
4148	parms = []
4149	for x in sel:
4150	parms.append(names[x])
4151	wx.BeginBusyCursor()
4152	try:
4153	for rbObj in RBObjs:
4154	if 'Origin' in parms:
4155	rbObj['Orig'][1] = True
4156	else:
4157	rbObj['Orig'][1] = False
4158	if 'Full Orient.' in parms:
4159	rbObj['Orient'][1] = 'AV'
4160	elif 'Orient. angle' in parms:
4161	rbObj['Orient'][1] = 'A'
4162	else:
4163	rbObj['Orient'][1] = ' '
4164	for i in range(len(rbObj['Torsions'])):
4165	if 'Torsion '+str(i) in parms:
4166	rbObj['Torsions'][i][1] = True
4167	else:
4168	rbObj['Torsions'][</